loqusdb 2.7.3__py3-none-any.whl → 2.7.8__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (55) hide show
  1. README.md +148 -0
  2. loqusdb/__init__.py +5 -3
  3. loqusdb/__main__.py +0 -0
  4. loqusdb/build_models/variant.py +12 -4
  5. loqusdb/resources/loqusdb.20181005.gz +0 -0
  6. loqusdb/resources/maf_50_sites_GRCh37.vcf.gz +0 -0
  7. loqusdb/resources/maf_50_sites_GRCh38.vcf.gz +0 -0
  8. {loqusdb-2.7.3.dist-info → loqusdb-2.7.8.dist-info}/METADATA +27 -42
  9. loqusdb-2.7.8.dist-info/RECORD +97 -0
  10. {loqusdb-2.7.3.dist-info → loqusdb-2.7.8.dist-info}/WHEEL +1 -2
  11. loqusdb-2.7.8.dist-info/entry_points.txt +3 -0
  12. tests/build_models/test_build_case.py +150 -0
  13. tests/build_models/test_build_variant.py +15 -0
  14. tests/build_models/test_is_greater.py +49 -0
  15. tests/commands/test_export.py +16 -0
  16. tests/commands/test_identity.py +22 -0
  17. tests/commands/test_view.py +17 -0
  18. tests/conftest.py +438 -0
  19. tests/fixtures/643594.clinical.SV.vcf +178 -0
  20. tests/fixtures/643594.clinical.vcf.gz +0 -0
  21. tests/fixtures/double_variant.vcf +21 -0
  22. tests/fixtures/funny_trio.ped +4 -0
  23. tests/fixtures/profile_snv.vcf +47 -0
  24. tests/fixtures/recessive_trio.ped +4 -0
  25. tests/fixtures/test.SV.vcf +178 -0
  26. tests/fixtures/test.vcf +26 -0
  27. tests/fixtures/test.vcf.gz +0 -0
  28. tests/fixtures/test.vcf.gz.tbi +0 -0
  29. tests/fixtures/unsorted.vcf +20 -0
  30. tests/functional/test_cli.py +213 -0
  31. tests/plugins/mongo/test_case_operations.py +143 -0
  32. tests/plugins/mongo/test_connect.py +8 -0
  33. tests/plugins/mongo/test_flask_extension.py +27 -0
  34. tests/plugins/mongo/test_get_sv.py +27 -0
  35. tests/plugins/mongo/test_load_svs.py +74 -0
  36. tests/plugins/mongo/test_variant_operations.py +278 -0
  37. tests/utils/test_case.py +34 -0
  38. tests/utils/test_delete.py +73 -0
  39. tests/utils/test_delete_family.py +30 -0
  40. tests/utils/test_delete_variant.py +74 -0
  41. tests/utils/test_get_family.py +13 -0
  42. tests/utils/test_load_database.py +52 -0
  43. tests/utils/test_load_family.py +69 -0
  44. tests/utils/test_load_variants.py +225 -0
  45. tests/utils/test_migrate.py +38 -0
  46. tests/utils/test_profiling.py +68 -0
  47. tests/vcf_tools/test_check_par.py +67 -0
  48. tests/vcf_tools/test_check_vcf.py +64 -0
  49. tests/vcf_tools/test_format_sv_variant.py +102 -0
  50. tests/vcf_tools/test_format_variant.py +113 -0
  51. tests/vcf_tools/test_vcf.py +63 -0
  52. loqusdb-2.7.3.dist-info/RECORD +0 -54
  53. loqusdb-2.7.3.dist-info/entry_points.txt +0 -3
  54. loqusdb-2.7.3.dist-info/top_level.txt +0 -1
  55. {loqusdb-2.7.3.dist-info → loqusdb-2.7.8.dist-info}/LICENSE +0 -0
tests/fixtures/test.SV.vcf ADDED
@@ -0,0 +1,178 @@
1
+ ##fileformat=VCFv4.2
2
+ ##ALT=<ID=BND,Description="Translocation Breakend">
3
+ ##ALT=<ID=DEL,Description="Deletion">
4
+ ##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
5
+ ##ALT=<ID=INS,Description="Insertion">
6
+ ##ALT=<ID=INV,Description="Inversion">
7
+ ##FILTER=<ID=MaxMQ0Frac,Description="For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4">
8
+ ##FILTER=<ID=MinGQ,Description="GQ score is less than 15 (filter applied at sample level and record level if all samples are filtered)">
9
+ ##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20">
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+ ##FILTER=<ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample.">
11
+ ##FILTER=<ID=PASS,Description="All filters passed">
12
+ ##FILTER=<ID=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation">
13
+ ##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
14
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
15
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
16
+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
17
+ ##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
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+ ##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999">
19
+ ##INFO=<ID=1000GAF,Number=.,Type=Float,Description="calculated field: 1000GAF">
20
+ ##INFO=<ID=AF,Number=A,Type=Float,Description="transfered from matched variants in /mnt/hds/proj/cust003/develop/references/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz">
21
+ ##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
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+ ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
23
+ ##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
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+ ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
25
+ ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoFtool|LoF|LoF_filter|LoF_flags|LoF_info">
26
+ ##INFO=<ID=Compounds,Number=.,Type=String,Description="List of compound pairs for this variant.The list is splitted on ',' family id is separated with compoundswith ':'. Compounds are separated with '|'.">
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+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
28
+ ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
29
+ ##INFO=<ID=GeneticModels,Number=.,Type=String,Description="':'-separated list of genetic models for this variant.">
30
+ ##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
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+ ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
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+ ##INFO=<ID=ID,Number=1,Type=String,Description="calculated by first of overlapping values in field ID from /mnt/hds/proj/cust003/develop/references/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz">
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+ ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
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+ ##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
35
+ ##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
36
+ ##INFO=<ID=JUNCTION_QUAL,Number=1,Type=Integer,Description="If the SV junction is part of an EVENT (ie. a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only">
37
+ ##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
38
+ ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
39
+ ##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
40
+ ##INFO=<ID=ModelScore,Number=.,Type=String,Description="PHRED score for genotype models.">
41
+ ##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
42
+ ##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
43
+ ##INFO=<ID=RankResult,Number=.,Type=String,Description="variant_length|Variant_call_quality_filter|Inheritance_Models|Consequence|variant_type|Gene_intolerance_prediction|allele_frequency">
44
+ ##INFO=<ID=RankScore,Number=.,Type=String,Description="The rank score for this variant in this family. family_id:rank_score.">
45
+ ##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
46
+ ##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
47
+ ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
48
+ ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
49
+ ##INFO=<ID=left_1000GAF,Number=.,Type=String,Description="1000 genomes frequency SV left interval">
50
+ ##INFO=<ID=left_AF,Number=A,Type=Float,Description="transfered from matched variants in /mnt/hds/proj/cust003/develop/references/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz at end left">
51
+ ##INFO=<ID=left_ID,Number=1,Type=String,Description="calculated by first of overlapping values in field ID from /mnt/hds/proj/cust003/develop/references/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz at end left">
52
+ ##INFO=<ID=most_severe_consequence,Number=.,Type=String,Description="Most severe genomic consequence.">
53
+ ##INFO=<ID=right_1000GAF,Number=.,Type=String,Description="1000 genomes frequency SV right interval">
54
+ ##INFO=<ID=right_AF,Number=A,Type=Float,Description="transfered from matched variants in /mnt/hds/proj/cust003/develop/references/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz at end right">
55
+ ##INFO=<ID=right_ID,Number=1,Type=String,Description="calculated by first of overlapping values in field ID from /mnt/hds/proj/cust003/develop/references/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz at end right">
56
+ ##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence)
57
+ ##LoF_filter=Reason for LoF not being HC
58
+ ##LoF_flags=Possible warning flags for LoF
59
+ ##LoF_info=Info used for LoF annotation
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+ ##LoFtool=LoFtool score for gene
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+ ##Software=<ID=genmod,Version=3.5.9,Date="2016-12-08 17:36",CommandLineOptions="processes=4 keyword=Annotation family_file=<open file '/mnt/hds/proj/bioinfo/develop/henrikS/643594-miptest/analysis/643594-miptest/643594-miptest.fam', mode 'r' at 0x7fc018606c00> family_type=cmms reduced_penetrance=<open file '/mnt/hds/proj/bioinfo/develop/references_4.0/cust003-CMMS-red-pen.txt.csv', mode 'r' at 0x7fc018606b70> outfile=<unopened file '/dev/stdout' w> temp_dir=/scratch/717377 variant_file=/scratch/717377/643594-miptest_sorted_md_brecal_comb_vep_parsed_SV.selected.vcf logger=<logging.Logger object at 0x7fc018338c50> vep=True">
62
+ ##VEP=v85 cache=/mnt/hds/proj/bioinfo/components/maintainance/miniconda/envs/mip4.0/ensembl-tools-release-85/cache/homo_sapiens/85_GRCh37 db=. ESP=20141103 HGMD-PUBLIC=20152 polyphen=2.2.2 regbuild=13 dbSNP=144 ClinVar=201507 assembly=GRCh37.p13 gencode=GENCODE 19 sift=sift5.2.2 genebuild=2011-04 COSMIC=71
63
+ ##bcftools_annotateCommand=annotate --header-lines /mnt/hds/proj/bioinfo/develop/references_4.0/vcfanno_headerLines.v1.0.txt /scratch/717374/643594-miptest_sorted_md_brecal_comb_SV_vt_filt_genmod_filter_vcfanno.vcf
64
+ ##bcftools_annotateVersion=1.3.1+htslib-1.3.1
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+ ##bcftools_concatCommand=concat -a /scratch/717374/643594-miptest_pmanta.vcf.gz
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+ ##bcftools_concatVersion=1.3.1+htslib-1.3.1
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+ ##bcftools_viewCommand=view -f PASS /scratch/717374/643594-miptest_sorted_md_brecal_comb_SV_vt.vcf
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+ ##bcftools_viewVersion=1.3.1+htslib-1.3.1
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+ ##cmdline=/mnt/hds/proj/bioinfo/components/maintainance/miniconda/envs/mip4.0/bin/configManta.py --bam /scratch/717373/ADM1059A1_lanes_1_sorted_md_brecal.bam --bam /scratch/717373/ADM1059A2_lanes_1_sorted_md_brecal.bam --bam /scratch/717373/ADM1059A3_lanes_1_sorted_md_brecal.bam --referenceFasta /mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta --exome --runDir /scratch/717373
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+ ##contig=<ID=1,length=249250621>
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+ ##contig=<ID=2,length=243199373>
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+ ##contig=<ID=3,length=198022430>
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+ ##contig=<ID=4,length=191154276>
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+ ##contig=<ID=5,length=180915260>
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+ ##contig=<ID=6,length=171115067>
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+ ##contig=<ID=7,length=159138663>
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+ ##contig=<ID=8,length=146364022>
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+ ##contig=<ID=9,length=141213431>
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+ ##contig=<ID=10,length=135534747>
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+ ##contig=<ID=11,length=135006516>
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+ ##contig=<ID=12,length=133851895>
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+ ##contig=<ID=13,length=115169878>
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+ ##contig=<ID=14,length=107349540>
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+ ##contig=<ID=15,length=102531392>
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+ ##contig=<ID=16,length=90354753>
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+ ##contig=<ID=17,length=81195210>
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+ ##contig=<ID=18,length=78077248>
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+ ##contig=<ID=19,length=59128983>
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+ ##contig=<ID=20,length=63025520>
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+ ##contig=<ID=21,length=48129895>
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+ ##contig=<ID=22,length=51304566>
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+ ##contig=<ID=X,length=155270560>
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+ ##contig=<ID=Y,length=59373566>
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+ ##contig=<ID=MT,length=16569>
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+ ##contig=<ID=GL000207.1,length=4262>
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+ ##contig=<ID=GL000226.1,length=15008>
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+ ##contig=<ID=GL000229.1,length=19913>
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+ ##contig=<ID=GL000231.1,length=27386>
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+ ##contig=<ID=GL000210.1,length=27682>
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+ ##contig=<ID=GL000239.1,length=33824>
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+ ##contig=<ID=GL000235.1,length=34474>
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+ ##contig=<ID=GL000201.1,length=36148>
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+ ##contig=<ID=GL000247.1,length=36422>
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+ ##contig=<ID=GL000245.1,length=36651>
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+ ##contig=<ID=GL000197.1,length=37175>
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+ ##contig=<ID=GL000203.1,length=37498>
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+ ##contig=<ID=GL000246.1,length=38154>
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+ ##contig=<ID=GL000249.1,length=38502>
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+ ##contig=<ID=GL000196.1,length=38914>
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+ ##contig=<ID=GL000248.1,length=39786>
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+ ##contig=<ID=GL000244.1,length=39929>
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+ ##contig=<ID=GL000202.1,length=40103>
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+ ##contig=<ID=GL000234.1,length=40531>
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+ ##contig=<ID=GL000232.1,length=40652>
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+ ##contig=<ID=GL000206.1,length=41001>
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+ ##contig=<ID=GL000240.1,length=41933>
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+ ##contig=<ID=GL000236.1,length=41934>
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+ ##contig=<ID=GL000241.1,length=42152>
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+ ##contig=<ID=GL000243.1,length=43341>
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+ ##contig=<ID=GL000242.1,length=43523>
122
+ ##contig=<ID=GL000230.1,length=43691>
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+ ##contig=<ID=GL000237.1,length=45867>
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+ ##contig=<ID=GL000233.1,length=45941>
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+ ##contig=<ID=GL000204.1,length=81310>
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+ ##contig=<ID=GL000198.1,length=90085>
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+ ##contig=<ID=GL000208.1,length=92689>
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+ ##contig=<ID=GL000191.1,length=106433>
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+ ##contig=<ID=GL000227.1,length=128374>
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+ ##contig=<ID=GL000218.1,length=161147>
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+ ##contig=<ID=GL000220.1,length=161802>
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+ ##contig=<ID=GL000213.1,length=164239>
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+ ##contig=<ID=GL000211.1,length=166566>
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+ ##contig=<ID=GL000199.1,length=169874>
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+ ##contig=<ID=GL000217.1,length=172149>
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+ ##contig=<ID=GL000216.1,length=172294>
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+ ##contig=<ID=GL000215.1,length=172545>
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+ ##contig=<ID=GL000205.1,length=174588>
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+ ##contig=<ID=GL000219.1,length=179198>
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+ ##contig=<ID=GL000224.1,length=179693>
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+ ##contig=<ID=GL000223.1,length=180455>
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+ ##contig=<ID=GL000195.1,length=182896>
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+ ##contig=<ID=GL000212.1,length=186858>
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+ ##contig=<ID=GL000222.1,length=186861>
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+ ##contig=<ID=GL000200.1,length=187035>
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+ ##contig=<ID=GL000193.1,length=189789>
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+ ##contig=<ID=GL000194.1,length=191469>
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+ ##contig=<ID=GL000225.1,length=211173>
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+ ##contig=<ID=GL000192.1,length=547496>
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+ ##contig=<ID=NC_007605,length=171823>
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+ ##contig=<ID=hs37d5,length=35477943>
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+ ##fileDate=20161208
157
+ ##reference=file:///mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta
158
+ ##source=GenerateSVCandidates 1.0.0
159
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father proband mother
160
+ 1 7889972 MantaDEL:1:0:0:0:0:0 GAGAATCCATCCCATCCTACTGCCAGCGCTCTGTCCACAGGATCGCCTCCCATGA G 383 PASS CIGAR=1M54D;CIPOS=0,80;CSQ=deletion|inframe_deletion&feature_truncation|MODERATE|PER3|ENSG00000049246|Transcript|ENST00000361923|protein_coding|18/21||||3114-3167|2939-2992|980-998|||||1||HGNC|8847|YES|||CCDS89.1|ENSP00000355031|P56645|Q8TAR6&B4DR65&A2I2N5|UPI0000167B1D|||Pfam_domain:PF12114&hmmpanther:PTHR11269&hmmpanther:PTHR11269:SF13||||||||||,deletion|inframe_deletion&feature_truncation|MODERATE|PER3|ENSG00000049246|Transcript|ENST00000377532|protein_coding|18/21||||3190-3243|2966-3019|989-1007|||||1||HGNC|8847|||||ENSP00000366755|P56645||UPI00003664CA|||hmmpanther:PTHR11269&hmmpanther:PTHR11269:SF13&Pfam_domain:PF12114||||||||||:ENST00000361923:inframe_deletion&feature_truncation:ENST00000377532:inframe_deletion&feature_truncation;END=7890026;HOMLEN=80;HOMSEQ=AGAATCCATCCCATCCTACTGCCAGCGCTCTGTCCACAGGATCGCCTCCCATGAAGAATCCATCCCATCCTACTGCCAGC;RankResult=8|0|-12|5|3|0|4;RankScore=643594:8;SVLEN=-54;SVTYPE=DEL;most_severe_consequence=8847:deletion|inframe_deletion GT:FT:GQ:PL:PR:SR 0/0:PASS:56:0,6,62:1,0:4,2 0/1:PASS:100:154,0,100:6,0:10,5 1/1:MinGQ:10:332,13,0:0,0:0,9
161
+ 4 861261 MantaDEL:10:0:0:0:0:0 CGGCCAGCACCAGGGTCCCCACGGCGCGTCCCTTCAGGGCCTCCTCGGCCCAGGGCCTTGGTGAACACACGT C 46 PASS CIGAR=1M71D;CIPOS=0,91;CSQ=deletion|intron_variant&feature_truncation|MODIFIER|GAK|ENSG00000178950|Transcript|ENST00000314167|protein_coding||20/27||||||||||-1||HGNC|4113|YES|||CCDS3340.1|ENSP00000314499|O14976|Q59HA5&D6RF16&D6RC24|UPI000012B04A|||||||||||||,deletion|intron_variant&non_coding_transcript_variant&feature_truncation|MODIFIER|GAK|ENSG00000178950|Transcript|ENST00000509566|processed_transcript||3/10||||||||||-1||HGNC|4113|||||||||||||||||||||,deletion|upstream_gene_variant|MODIFIER|GAK|ENSG00000178950|Transcript|ENST00000510799|protein_coding|||||||||||256|-1|cds_start_NF&cds_end_NF|HGNC|4113|||||ENSP00000426062|||UPI0001D3B0C9|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|GAK|ENSG00000178950|Transcript|ENST00000511163|protein_coding||17/24||||||||||-1||HGNC|4113|||||ENSP00000421361||E9PGR2&D6RF16|UPI000020B996|||||||||||||,deletion|upstream_gene_variant|MODIFIER|GAK|ENSG00000178950|Transcript|ENST00000511980|protein_coding|||||||||||312|-1|cds_start_NF|HGNC|4113|||||ENSP00000421049|||UPI0001D3B0C8|||||||||||||,deletion|intron_variant&non_coding_transcript_variant&feature_truncation|MODIFIER|GAK|ENSG00000178950|Transcript|ENST00000515868|retained_intron||1/6||||||||||-1||HGNC|4113|||||||||||||||||||||:ENST00000314167:intron_variant&feature_truncation:ENST00000509566:intron_variant&non_coding_transcript_variant&feature_truncation:ENST00000510799:upstream_gene_variant:ENST00000511163:intron_variant&feature_truncation:ENST00000511980:upstream_gene_variant:ENST00000515868:intron_variant&non_coding_transcript_variant&feature_truncation;END=861332;GeneticModels=643594:AD_dn;HOMLEN=91;HOMSEQ=GGCCAGCACCAGGGTCCCCACGGCGCGTCCCTTCAGGGCCTCCTCGGCCCAGGGCCTTGGTGAACACACGTGGCCAGCACCAGGGTCCCCA;ModelScore=643594:15;RankResult=8|-5|1|1|3|0|4;RankScore=643594:12;SVLEN=-71;SVTYPE=DEL;most_severe_consequence=4113:deletion|non_coding_transcript_variant GT:FT:GQ:PL:PR:SR 0/0:PASS:61:0,11,102:1,0:3,1 0/1:PASS:46:96,0,64:0,0:2,6 0/0:PASS:15:35,0,68:1,0:2,2
162
+ 5 474602 MantaDEL:14:0:0:0:0:0 GCGGGGAGAGAGAGAGAGCGAGCCAGGTTCAGGTCCAGGGAGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGGGAGGGAGAGAGCCAGGTTCAGGTCCAGGGAGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGGGAGAGAGAGAGCGAGCCAGGTTCAGGTCCAGGGAGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGGGAGGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGC GT 847 PASS CIGAR=1M1I372D;CSQ=deletion|intron_variant&feature_truncation|MODIFIER|SLC9A3|ENSG00000066230|Transcript|ENST00000264938|protein_coding||16/16||||||||||-1||HGNC|11073|YES|||CCDS3855.1|ENSP00000264938|P48764||UPI000013D597|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SLC9A3|ENSG00000066230|Transcript|ENST00000507407|retained_intron|||||||||||4778|-1||HGNC|11073|||||||||||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SLC9A3|ENSG00000066230|Transcript|ENST00000514375|protein_coding||16/16||||||||||-1||HGNC|11073||||CCDS64116.1|ENSP00000422983||E9PF67|UPI0001D3B0BF|||||||||||||:ENST00000264938:intron_variant&feature_truncation:ENST00000507407:downstream_gene_variant:ENST00000514375:intron_variant&feature_truncation;END=474974;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=-372;SVTYPE=DEL;left_1000GAF=0.0003993599966634065;left_AF=0.00039936;left_ID=DUP_uwash_chr5_359687_478235;most_severe_consequence=11073:deletion|intron_variant;right_1000GAF=0.0003993599966634065;right_AF=0.00039936;right_ID=DUP_uwash_chr5_359687_478235 GT:FT:GQ:PL:PR:SR 1/1:MinGQ:3:535,4,0:0,0:0,18 0/1:PASS:27:270,0,24:0,0:0,16 0/1:PASS:47:193,0,44:0,0:5,6
163
+ 6 4050241 MantaDEL:19:0:0:0:0:0 TGGAAACAGTTGTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAATAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCACAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCA T 999 PASS 1000GAF=0.6713;AF=0.6713;CIGAR=1M319D;CIPOS=0,16;CSQ=deletion|intron_variant&feature_truncation|MODIFIER|PRPF4B|ENSG00000112739|Transcript|ENST00000337659|protein_coding||9/14||||||||||1||HGNC|17346|YES|||CCDS4488.1|ENSP00000337194|Q13523|H0YDJ3&F5H2U2|UPI000013DD12|||||||||||||,deletion|intron_variant&non_coding_transcript_variant&feature_truncation|MODIFIER|PRPF4B|ENSG00000112739|Transcript|ENST00000463634|retained_intron||6/16||||||||||1||HGNC|17346|||||||||||||||||||||,deletion|upstream_gene_variant|MODIFIER|PRPF4B|ENSG00000112739|Transcript|ENST00000466185|processed_transcript|||||||||||1656|1||HGNC|17346|||||||||||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PRPF4B|ENSG00000112739|Transcript|ENST00000480058|nonsense_mediated_decay||9/15||||||||||1||HGNC|17346||||CCDS4488.1|ENSP00000433547|Q13523|H0YDJ3&F5H2U2|UPI000013DD12|||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PRPF4B|ENSG00000112739|Transcript|ENST00000481109|nonsense_mediated_decay||7/18||||||||||1|cds_start_NF|HGNC|17346|||||ENSP00000433714||H0YDJ3|UPI00004A3980|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|PRPF4B|ENSG00000112739|Transcript|ENST00000538861|protein_coding||9/14||||||||||1||HGNC|17346|||||ENSP00000439331||H0YDJ3&F5H2U2|UPI0000141292|||||||||||||:ENST00000337659:intron_variant&feature_truncation:ENST00000463634:intron_variant&non_coding_transcript_variant&feature_truncation:ENST00000466185:upstream_gene_variant:ENST00000480058:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000481109:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000538861:intron_variant&feature_truncation;END=4050560;HOMLEN=16;HOMSEQ=GGAAACAGTTGTTTTT;ID=DEL_pindel_18082;RankResult=8|0|-12|1|3|0|-6;RankScore=643594:-6;SVLEN=-319;SVTYPE=DEL;left_1000GAF=0.6712999939918518;left_AF=0.6713;left_ID=DEL_pindel_18082;most_severe_consequence=17346:deletion|non_coding_transcript_variant;right_1000GAF=0.6712999939918518;right_AF=0.6713;right_ID=DEL_pindel_18082 GT:FT:GQ:PL:PR:SR 1/1:PASS:48:848,51,0:0,0:0,24 1/1:PASS:48:853,51,0:0,0:0,21 0/1:MinGQ:4:296,2,0:0,0:0,11
164
+ 7 144343218 MantaINS:22:0:0:0:0:0 T TTCTTATGAATTTATCTCATCTCCCCTCAAGCCTCATGAAGAATTTAAAGTTTTGTGATTTCAATACCTTATGTTTCTTTTTAAAACAATGTGTACTTTGATAATGCCAGTTTAGAATTAAACACAGATGATGGTGTTGTGGTTAGAAGAATTACCAATGCTATAATTTTTATTTGAAAAAGTTTTCATTGTCTTCCAAAACCACTGAGACCTTGAATTATTGGTTACTTTAATACACTCTCACGTGACTTATATCATTCCCAATTAGATTATTTATATGTTCTTAAGTGGCAAGGA 861 PASS CIGAR=1M296I;CIPOS=0,4;CSQ=insertion|intron_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000360057|protein_coding||5/8||||||||||-1||HGNC|17358|YES|||CCDS5888.1|ENSP00000353165|Q9H3S4|Q75MX1&F8VRJ6|UPI000004FD50|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000378098|nonsense_mediated_decay||5/9||||||||||-1||HGNC|17358|||||ENSP00000367338||F8WCM7|UPI00018814B8|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000378099|protein_coding||5/7||||||||||-1||HGNC|17358||||CCDS55178.1|ENSP00000367339||F5GZG6|UPI00001AEE82|||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000481645|retained_intron||3/3||||||||||-1||HGNC|17358|||||||||||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000482940|nonsense_mediated_decay||6/11||||||||||-1||HGNC|17358|||||ENSP00000449909||F8VVJ1|UPI000020F23A|||||||||||||,insertion|3_prime_UTR_variant&NMD_transcript_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000489798|nonsense_mediated_decay|5/6||||370-371|||||||-1||HGNC|17358|||||ENSP00000450028||F8VPB3|UPI00020CDF2E|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000538212|protein_coding||4/6||||||||||-1||HGNC|17358|||||ENSP00000438813||Q6ZQX6|UPI00001C105E|||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000547966|processed_transcript||2/5||||||||||-1||HGNC|17358|||||||||||||||||||||,insertion|upstream_gene_variant|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000548831|processed_transcript|||||||||||11|-1||HGNC|17358|||||||||||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000549981|protein_coding||6/11||||||||||-1||HGNC|17358|||||ENSP00000448698||I6L9B8|UPI000056F1AD|||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000551062|processed_transcript||2/4||||||||||-1||HGNC|17358|||||||||||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|TPK1|ENSG00000196511|Transcript|ENST00000552881|protein_coding||5/6||||||||||-1|cds_end_NF|HGNC|17358|||||ENSP00000448655||F8VRJ6|UPI00020CDF2D|||||||||||||:ENST00000360057:intron_variant&feature_elongation:ENST00000378098:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000378099:intron_variant&feature_elongation:ENST00000481645:intron_variant&non_coding_transcript_variant&feature_elongation:ENST00000482940:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000489798:3_prime_UTR_variant&NMD_transcript_variant&feature_elongation:ENST00000538212:intron_variant&feature_elongation:ENST00000547966:intron_variant&non_coding_transcript_variant&feature_elongation:ENST00000548831:upstream_gene_variant:ENST00000549981:intron_variant&feature_elongation:ENST00000551062:intron_variant&non_coding_transcript_variant&feature_elongation:ENST00000552881:intron_variant&feature_elongation;END=144343218;HOMLEN=4;HOMSEQ=TCTT;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=296;SVTYPE=INS;most_severe_consequence=17358:insertion|3_prime_UTR_variant GT:FT:GQ:PL:PR:SR 0/0:PASS:118:0,68,999:2,0:22,0 0/0:PASS:127:0,77,999:6,0:25,0 0/1:PASS:725:911,0,722:2,1:16,28
165
+ 8 133920667 MantaINS:24:0:0:0:10:0 A <INS> 999 PASS CIEND=0,1;CIPOS=0,1;CSQ=insertion|intron_variant&feature_elongation|MODIFIER|TG|ENSG00000042832|Transcript|ENST00000220616|protein_coding||18/47||||||||||1||HGNC|11764|YES|||CCDS34944.1|ENSP00000220616|P01266|Q9NYM1&Q9NYD9&E5RG33|UPI000013C79F|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|TG|ENSG00000042832|Transcript|ENST00000377869|protein_coding||18/46||||||||||1||HGNC|11764|||||ENSP00000367100|P01266|Q9NYM1&Q9NYD9&E5RG33|UPI0000D62505|||||||||||||,insertion|downstream_gene_variant|MODIFIER|TG|ENSG00000042832|Transcript|ENST00000518505|protein_coding|||||||||||1522|1|cds_start_NF&cds_end_NF|HGNC|11764|||||ENSP00000429605|||UPI0001E8F422|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|TG|ENSG00000042832|Transcript|ENST00000523756|nonsense_mediated_decay||5/34||||||||||1|cds_start_NF|HGNC|11764|||||ENSP00000428628|||UPI0001E8F41E|||||||||||||:ENST00000220616:intron_variant&feature_elongation:ENST00000377869:intron_variant&feature_elongation:ENST00000518505:downstream_gene_variant:ENST00000523756:intron_variant&NMD_transcript_variant&feature_elongation;END=133920667;HOMLEN=1;HOMSEQ=C;LEFT_SVINSSEQ=CCTGAGGGTTTGAGTTCAACCCTCACTGTTTTATCAATGTGCAAAAACA;RIGHT_SVINSSEQ=ACAGGAAAGGGAGTTAGTCCAAGTAAAACCCATCCAGGTTTGCTAACTGGTGCTATTGCAGCCTCC;RankResult=0|0|-12|1|3|0|4;RankScore=643594:-4;SVTYPE=INS;most_severe_consequence=11764:insertion|intron_variant GT:FT:GQ:PL:PR:SR 1/1:PASS:27:465,30,0:0,0:0,10 1/1:PASS:39:668,42,0:0,0:0,14 1/1:PASS:47:752,50,0:0,0:0,17
166
+ 8 141468110 MantaDEL:27:0:0:0:0:1 GAGGAGAGTAGGAGGAGGAGGGGTGAAAGAAGGAGGGAGGGGCAGCGAGAGAGAGAAGCGGGGGAC G 41 PASS CIGAR=1M65D;CIPOS=0,3;CSQ=deletion|upstream_gene_variant|MODIFIER|TRAPPC9|ENSG00000167632|Transcript|ENST00000389327|protein_coding|||||||||||250|-1||HGNC|30832|||||ENSP00000373978|Q96Q05||UPI0000E5AF77|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|TRAPPC9|ENSG00000167632|Transcript|ENST00000389328|protein_coding||1/22||||||||||-1||HGNC|30832|YES|||CCDS34946.1|ENSP00000373979|Q96Q05||UPI0000DBEF2B|||||||||||||,deletion|upstream_gene_variant|MODIFIER|TRAPPC9|ENSG00000167632|Transcript|ENST00000438773|protein_coding|||||||||||250|-1||HGNC|30832||||CCDS55278.1|ENSP00000405060|Q96Q05||UPI00001A46C7|||||||||||||:ENST00000389327:upstream_gene_variant:ENST00000389328:intron_variant&feature_truncation:ENST00000438773:upstream_gene_variant;END=141468175;GeneticModels=643594:AD_dn;HOMLEN=3;HOMSEQ=AGG;ModelScore=643594:6;RankResult=8|-5|1|1|3|0|4;RankScore=643594:12;SVLEN=-65;SVTYPE=DEL;left_1000GAF=0.000998400035314262;left_AF=0.0009984;left_ID=DUP_delly_DUP80162;most_severe_consequence=30832:deletion|intron_variant;right_1000GAF=0.000998400035314262;right_AF=0.0009984;right_ID=DUP_delly_DUP80162 GT:FT:GQ:PL:PR:SR 0/0:MinGQ:6:46,0,98:0,0:2,3 0/1:PASS:40:90,0,53:0,0:1,3 0/0:PASS:56:0,6,27:0,0:2,0
167
+ 9 133305073 MantaDEL:29:0:0:0:2:0 GTACGGGGACACCCACCCTCTGGCCACACCGCTGCAGCTGCCCCAGGGGTTACCGGATGCAGGGCCCCAGCCTGCCCTGCCTAGT G 142 PASS CIGAR=1M84D;CIPOS=0,25;CSQ=deletion|upstream_gene_variant|MODIFIER|HMCN2|ENSG00000148357|Transcript|ENST00000302481|protein_coding|||||||||||512|1||HGNC|21293|||||ENSP00000305590|Q8NDA2||UPI0000073F38|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|HMCN2|ENSG00000148357|Transcript|ENST00000428715|protein_coding||10/13||||||||||1||HGNC|21293|YES||||ENSP00000387564||H0Y3X1|UPI0001881428|||||||||||||:ENST00000302481:upstream_gene_variant:ENST00000428715:intron_variant&feature_truncation;END=133305157;HOMLEN=25;HOMSEQ=TACGGGGACACCCACCCTCTGGCCA;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=-84;SVTYPE=DEL;most_severe_consequence=21293:deletion|intron_variant GT:FT:GQ:PL:PR:SR 0/0:PASS:81:0,31,216:2,0:10,0 0/1:PASS:58:108,0,71:1,0:5,5 1/1:MinGQ:7:136,9,0:0,0:0,4
168
+ 11 223831 MantaDEL:31:0:0:0:0:0 GCCTCCTCCCTGCACAGGCCTGCCGACAGCCCATGAGATGACTCCTGTACCCCTCCCTTCCCCTGCCCTCCAGCCTCCTCCCTGCACAGGCCTGCCGACAGCCCATGAGGTGACTCCTGTACCCCTCCCTTCCCCTGCCCTCCAGACTCCTCCCTGCACAGGCCTGCCGACAGCCCATGAGATGACTCCTGTACCCCTCCCTTCCCCTGCCCTCCAGC GA 446 PASS CIGAR=1M1I217D;CSQ=deletion|intron_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000382743|protein_coding||5/6||||||||||-1||HGNC|14931|YES|||CCDS7691.1|ENSP00000372191|Q9NTG7|E9PNA0&E9PM52|UPI0000073D3C|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000524564|protein_coding||4/5||||||||||-1||HGNC|14931|||||ENSP00000432937||E9PN58|UPI0001F786DA|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000525319|protein_coding||5/6||||||||||-1||HGNC|14931|||||ENSP00000435464||E9PNA0&E9PM52&E9PK80|UPI0001F786D9|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000526854|nonsense_mediated_decay|||||||||||119|-1||HGNC|14931|||||ENSP00000435505||E9PJS6|UPI0001F786DC|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000528702|processed_transcript|||||||||||1625|-1||HGNC|14931|||||||||||||||||||||,deletion|downstream_gene_variant|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000529055|nonsense_mediated_decay|||||||||||174|-1||HGNC|14931|||||ENSP00000437179||E9PIT6|UPI0001F786D8|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000529382|protein_coding||5/6||||||||||-1||HGNC|14931||||CCDS53590.1|ENSP00000437216|Q9NTG7|E9PNA0&E9PM52|UPI00003D05E4|||||||||||||,deletion|coding_sequence_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000529937|nonsense_mediated_decay|3/5|2/4|||?-336|?-327|?-109|||||-1||HGNC|14931|||||ENSP00000434747||B7WNN4|UPI00015DFF48|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000531753|processed_transcript|||||||||||42|-1||HGNC|14931|||||||||||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000532837|nonsense_mediated_decay||5/6||||||||||-1||HGNC|14931|||||ENSP00000433899||E9PIT6|UPI0001F786D8|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000532956|protein_coding||4/5||||||||||-1||HGNC|14931|||||ENSP00000433077||E9PNA0&E9PM75&E9PM52|UPI0001F786DB|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SIRT3|ENSG00000142082|Transcript|ENST00000534381|retained_intron|||||||||||1714|-1||HGNC|14931|||||||||||||||||||||:ENST00000382743:intron_variant&feature_truncation:ENST00000524564:intron_variant&feature_truncation:ENST00000525319:intron_variant&feature_truncation:ENST00000526854:downstream_gene_variant:ENST00000528702:downstream_gene_variant:ENST00000529055:downstream_gene_variant:ENST00000529382:intron_variant&feature_truncation:ENST00000529937:coding_sequence_variant&intron_variant&NMD_transcript_variant&feature_truncation:ENST00000531753:downstream_gene_variant:ENST00000532837:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000532956:intron_variant&feature_truncation:ENST00000534381:downstream_gene_variant;END=224048;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=-217;SVTYPE=DEL;left_1000GAF=0.000599040009547025;left_AF=0.00059904;left_ID=DUP_uwash_chr11_194412_252166;most_severe_consequence=14931:deletion|coding_sequence_variant;right_1000GAF=0.000599040009547025;right_AF=0.00059904;right_ID=DUP_uwash_chr11_194412_252166 GT:FT:GQ:PL:PR:SR 0/0:PASS:189:0,139,999:10,4:47,0 0/1:PASS:252:302,0,390:3,11:12,14 0/1:PASS:142:243,0,139:0,16:4,14
169
+ 13 21729289 MantaDEL:39:0:0:0:0:0 TCTGCAACAGATACAAATAACAAATATCAATTTAATAAAATTAAAAGCCATTAAGACAAATGACACAATACTGTGGCTATATATTTTACACTTATAAAATAATTGAGGATAGATTCCCACTGATATCATTAAACTGGATAATTCGGGAATCTGAGATTCAGGGATCACAAGTTCTATATCAAAAGATAGAGACAGGCTATTAACTTAAGCTGGCAAATGTCAATTAAAAACAAAATTTTTACCAATATTCAAATGTTAATTTTTTTTTTTTTTTTTTAGATGGAGTCTCGCTCTGTTGCCAGGCTGGAGTGCAGTGGCATGATCTTGGCTCACTGCAACCTCCGCCTCCCAGATTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTGCACCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACGAGGTTTCACCATGTTGGTCAGGATGGTCAAATGTTAATTTTTAAATGTCCTCCTCAAATAACACATGAACTTTCTTTACAAAGGTAACATACTCAC T 521 PASS CIGAR=1M542D;CIPOS=0,1;CSQ=deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000298260|nonsense_mediated_decay||7/7||||||||||-1||HGNC|20262|||||ENSP00000298260|Q8IX90||UPI0001F4E027|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000314759|protein_coding||8/8||||||||||-1||HGNC|20262|YES|||CCDS31946.1|ENSP00000319417|Q8IX90||UPI00001AEC75|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000400018|protein_coding||7/7||||||||||-1||HGNC|20262||||CCDS53856.1|ENSP00000382896|Q8IX90||UPI000006F83C|||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000462482|nonsense_mediated_decay||2/2||||||||||-1||HGNC|20262|||||ENSP00000443543||F5H8H7|UPI000204AA68|||||||||||||:ENST00000298260:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000314759:intron_variant&feature_truncation:ENST00000400018:intron_variant&feature_truncation:ENST00000462482:intron_variant&NMD_transcript_variant&feature_truncation;END=21729831;HOMLEN=1;HOMSEQ=C;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=-542;SVTYPE=DEL;most_severe_consequence=20262:deletion|intron_variant GT:FT:GQ:PL:PR:SR 0/0:PASS:251:0,201,999:14,0:66,0 0/0:PASS:262:0,212,999:19,0:63,0 0/1:PASS:521:571,0,999:10,4:43,18
170
+ 13 21732261 MantaDEL:39:3:4:0:5:0 A <DEL> 454 PASS CIEND=0,4;CIPOS=0,4;CSQ=deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000298260|nonsense_mediated_decay|6/8|5/7|||?-927|||||||-1||HGNC|20262|||||ENSP00000298260|Q8IX90||UPI0001F4E027|||||||||||||,deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000314759|protein_coding|7/9|6/8|||?-1043|?-918|?-306|||||-1||HGNC|20262|YES|||CCDS31946.1|ENSP00000319417|Q8IX90||UPI00001AEC75|||||||||||||,deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000400018|protein_coding|7/8|6/7|||?-988|?-918|?-306|||||-1||HGNC|20262||||CCDS53856.1|ENSP00000382896|Q8IX90||UPI000006F83C|||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000462482|nonsense_mediated_decay||1/2||||||||||-1||HGNC|20262|||||ENSP00000443543||F5H8H7|UPI000204AA68|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000465471|nonsense_mediated_decay|||||||||||1892|-1||HGNC|20262|||||ENSP00000441632||F5GWG1|UPI000204AA69|||||||||||||:ENST00000298260:3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation:ENST00000314759:coding_sequence_variant&intron_variant&feature_truncation:ENST00000400018:coding_sequence_variant&intron_variant&feature_truncation:ENST00000462482:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000465471:downstream_gene_variant;END=21734037;HOMLEN=4;HOMSEQ=TACC;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=-1776;SVTYPE=DEL;most_severe_consequence=20262:deletion|coding_sequence_variant GT:FT:GQ:PL:PR:SR 0/0:PASS:192:0,142,999:12,0:43,0 0/0:PASS:237:0,187,999:12,0:60,0 0/1:PASS:454:504,0,999:14,5:62,19
171
+ 13 21732265 MantaDEL:39:3:6:0:0:0 C <DEL> 272 PASS CSQ=deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000298260|nonsense_mediated_decay|5/8|4-5/7||||||||||-1||HGNC|20262|||||ENSP00000298260|Q8IX90||UPI0001F4E027|||||||||||||,deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000314759|protein_coding|6/9|5-6/8||||||||||-1||HGNC|20262|YES|||CCDS31946.1|ENSP00000319417|Q8IX90||UPI00001AEC75|||||||||||||,deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000400018|protein_coding|6/8|5-6/7||||||||||-1||HGNC|20262||||CCDS53856.1|ENSP00000382896|Q8IX90||UPI000006F83C|||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000462482|nonsense_mediated_decay||1/2||||||||||-1||HGNC|20262|||||ENSP00000443543||F5H8H7|UPI000204AA68|||||||||||||,deletion|downstream_gene_variant|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000465471|nonsense_mediated_decay|||||||||||1|-1||HGNC|20262|||||ENSP00000441632||F5GWG1|UPI000204AA69|||||||||||||:ENST00000298260:3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation:ENST00000314759:coding_sequence_variant&intron_variant&feature_truncation:ENST00000400018:coding_sequence_variant&intron_variant&feature_truncation:ENST00000462482:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000465471:downstream_gene_variant;END=21735928;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVINSLEN=85;SVINSSEQ=AAAGCTATGCTGTTCTTTGTAGATGGAATTTTCAAACCAGGAGTACAGAATGTAGGTACCAAAGGAGAGTTGGTATATTCGGCAT;SVLEN=-3663;SVTYPE=DEL;most_severe_consequence=20262:deletion|coding_sequence_variant GT:FT:GQ:PL:PR:SR 0/0:PASS:211:0,161,999:16,0:53,0 0/0:PASS:235:0,185,999:14,0:61,0 0/1:PASS:272:322,0,999:16,3:58,16
172
+ 13 21746642 MantaDEL:39:10:11:0:0:0 T <DEL> 185 PASS CIEND=0,2;CIPOS=0,2;CSQ=deletion|coding_sequence_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000298260|nonsense_mediated_decay|2/8|1/7|||?-175|?-104|?-35|||||-1||HGNC|20262|||||ENSP00000298260|Q8IX90||UPI0001F4E027|||||||||||||,deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000314759|protein_coding|2-3/9|1-2/8|||?-291|?-166|?-56|||||-1||HGNC|20262|YES|||CCDS31946.1|ENSP00000319417|Q8IX90||UPI00001AEC75|||||||||||||,deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000400018|protein_coding|2-3/8|1-2/7|||?-236|?-166|?-56|||||-1||HGNC|20262||||CCDS53856.1|ENSP00000382896|Q8IX90||UPI000006F83C|||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000462482|nonsense_mediated_decay||1/2||||||||||-1||HGNC|20262|||||ENSP00000443543||F5H8H7|UPI000204AA68|||||||||||||,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|HIGH|SKA3|ENSG00000165480|Transcript|ENST00000465471|nonsense_mediated_decay|1-3/5|1-2/4|||179-267|105-?|35-?|||||-1||HGNC|20262|||||ENSP00000441632||F5GWG1|UPI000204AA69|||||||||||||,deletion|non_coding_transcript_exon_variant&intron_variant&non_coding_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000475251|retained_intron|2-3/3|1-2/2|||?-162|||||||-1||HGNC|20262|||||||||||||||||||||,deletion|non_coding_transcript_exon_variant&intron_variant&non_coding_transcript_variant&feature_truncation|MODIFIER|SKA3|ENSG00000165480|Transcript|ENST00000536239|retained_intron|1-2/3|1/2|||?-95|||||||-1||HGNC|20262|||||||||||||||||||||:ENST00000298260:coding_sequence_variant&intron_variant&NMD_transcript_variant&feature_truncation:ENST00000314759:coding_sequence_variant&intron_variant&feature_truncation:ENST00000400018:coding_sequence_variant&intron_variant&feature_truncation:ENST00000462482:intron_variant&NMD_transcript_variant&feature_truncation:ENST00000465471:stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation:ENST00000475251:non_coding_transcript_exon_variant&intron_variant&non_coding_transcript_variant&feature_truncation:ENST00000536239:non_coding_transcript_exon_variant&intron_variant&non_coding_transcript_variant&feature_truncation;END=21750512;HOMLEN=2;HOMSEQ=CC;RankResult=8|0|-12|8|3|0|4;RankScore=643594:11;SVLEN=-3870;SVTYPE=DEL;left_1000GAF=0.00019967999833170325;left_AF=0.00019968;left_ID=UW_VH_13782;most_severe_consequence=20262:deletion|stop_lost;right_1000GAF=0.00019967999833170325;right_AF=0.00019968;right_ID=UW_VH_13782 GT:FT:GQ:PL:PR:SR 0/0:PASS:268:0,218,999:26,0:63,0 0/0:PASS:209:0,159,999:20,0:49,0 0/1:PASS:185:235,0,999:31,3:57,9
173
+ 15 66633812 MantaDEL:43:0:0:0:0:0 TAAGAATGTTGTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAA T 975 PASS 1000GAF=0.8153;AF=0.8153;CIGAR=1M321D;CIPOS=0,12;CSQ=deletion|intron_variant&feature_truncation|MODIFIER|TIPIN|ENSG00000075131|Transcript|ENST00000261881|protein_coding||6/7||||||||||-1||HGNC|30750|YES|||CCDS10215.1|ENSP00000261881|Q9BVW5|H3BVG9&H3BU04&G8JLE5|UPI000013D21A|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|TIPIN|ENSG00000075131|Transcript|ENST00000367709|protein_coding||5/6||||||||||-1||HGNC|30750|||||ENSP00000356682||G8JLE5|UPI0000E59C7F|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|TIPIN|ENSG00000075131|Transcript|ENST00000562124|protein_coding||6/7||||||||||-1|cds_end_NF|HGNC|30750|||||ENSP00000457406||H3BVG9&H3BU04|UPI000246735A|||||||||||||,deletion|intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|TIPIN|ENSG00000075131|Transcript|ENST00000566524|nonsense_mediated_decay||5/6||||||||||-1||HGNC|30750|||||ENSP00000455656||H3BQ83|UPI0000E020D1|||||||||||||:ENST00000261881:intron_variant&feature_truncation:ENST00000367709:intron_variant&feature_truncation:ENST00000562124:intron_variant&feature_truncation:ENST00000566524:intron_variant&NMD_transcript_variant&feature_truncation;END=66634133;HOMLEN=12;HOMSEQ=AAGAATGTTGTG;ID=DEL_pindel_42359;RankResult=8|0|-12|1|3|0|-6;RankScore=643594:-6;SVLEN=-321;SVTYPE=DEL;left_1000GAF=0.8152999877929688;left_AF=0.8153;left_ID=DEL_pindel_42359;most_severe_consequence=30750:deletion|intron_variant;right_1000GAF=0.8152999877929688;right_AF=0.8153;right_ID=DEL_pindel_42359 GT:FT:GQ:PL:PR:SR 1/1:MinGQ:10:465,12,0:0,0:0,15 1/1:PASS:30:506,33,0:0,0:0,11 0/1:MinGQ:13:160,0,10:0,0:0,7
174
+ 16 4847619 MantaINS:44:0:0:0:0:0 T TGGGGTACACCAGACCCCAAGACTGGGGCGCTCTGAGGGCGTGGCAGGGCCCTCAGAACCCCTGCCCACTGTG 466 PASS CIGAR=1M72I;CIPOS=0,20;CSQ=insertion|intron_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000322048|protein_coding||10/10||||||||||-1||HGNC|29478|YES|||CCDS10523.1|ENSP00000322832|Q9GZN7|D3DUE5|UPI0000037B8E|||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000585653|retained_intron|||||||||||885|-1||HGNC|29478|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000585871|retained_intron|||||||||||3410|-1||HGNC|29478|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000586153|protein_coding|||||||||||102|-1|cds_start_NF|HGNC|29478|||||ENSP00000464699||K7EID1|UPI00028411F0|||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000586336|processed_transcript|||||||||||123|-1||HGNC|29478|||||||||||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000586504|protein_coding||6/6||||||||||-1|cds_start_NF&cds_end_NF|HGNC|29478|||||ENSP00000465076|||UPI00028411ED|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000587377|nonsense_mediated_decay||10/10||||||||||-1||HGNC|29478|||||ENSP00000468343||K7ERP1|UPI0000D4E582|||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000587711|protein_coding|||||||||||88|-1|cds_end_NF|HGNC|29478|||||ENSP00000467459||K7EPN1|UPI00028411EF|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000587843|nonsense_mediated_decay||9/9||||||||||-1||HGNC|29478|||||ENSP00000465970||K7EL91|UPI0002466D8D|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000588201|nonsense_mediated_decay||10/10||||||||||-1||HGNC|29478|||||ENSP00000466529||K7EMJ5|UPI00004DD952|||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000589543|retained_intron|||||||||||161|-1||HGNC|29478|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000590198|retained_intron|||||||||||3714|-1||HGNC|29478|||||||||||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000591292|retained_intron||6/6||||||||||-1||HGNC|29478|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000591392|protein_coding|||||||||||84|-1|cds_end_NF|HGNC|29478|||||ENSP00000467509||K7EPS3|UPI00028411EE|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000592019|protein_coding||3/3||||||||||-1|cds_start_NF|HGNC|29478|||||ENSP00000468334|||UPI00028411EC|||||||||||||,insertion|downstream_gene_variant|MODIFIER|ROGDI|ENSG00000067836|Transcript|ENST00000592112|retained_intron|||||||||||4197|-1||HGNC|29478|||||||||||||||||||||:ENST00000322048:intron_variant&feature_elongation:ENST00000585653:downstream_gene_variant:ENST00000585871:downstream_gene_variant:ENST00000586153:downstream_gene_variant:ENST00000586336:downstream_gene_variant:ENST00000586504:intron_variant&feature_elongation:ENST00000587377:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000587711:downstream_gene_variant:ENST00000587843:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000588201:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000589543:downstream_gene_variant:ENST00000590198:downstream_gene_variant:ENST00000591292:intron_variant&non_coding_transcript_variant&feature_elongation:ENST00000591392:downstream_gene_variant:ENST00000592019:intron_variant&feature_elongation:ENST00000592112:downstream_gene_variant;END=4847619;HOMLEN=20;HOMSEQ=GGGGTACACCAGACCCCAAG;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=72;SVTYPE=INS;most_severe_consequence=29478:insertion|non_coding_transcript_variant GT:FT:GQ:PL:PR:SR 0/1:PASS:356:516,0,353:0,0:10,18 0/0:PASS:105:0,55,768:0,0:19,0 0/0:PASS:121:0,71,837:0,0:25,0
175
+ 17 17719503 MantaINS:50:0:0:0:1:0 G GCCCCCCAACCCCCCCACCCCCGCCACCCCACACCCCTGCCACCCCCCAGCCCCACCCCCCCACCCCCAATCCCCCCACCCTCCCCACTCCCGCCAT 999 PASS CIGAR=1M96I;CIPOS=0,11;CSQ=insertion|intron_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000261646|protein_coding||11/18||||||||||-1||HGNC|11289||||CCDS11189.1|ENSP00000261646|P36956|J3QLB6&B5MD58|UPI0000141126|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000338854|protein_coding||11/18||||||||||-1||HGNC|11289|||||ENSP00000345822|P36956|J3QLB6|UPI0000366BAF|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000355815|protein_coding||12/19||||||||||-1||HGNC|11289|YES|||CCDS32583.1|ENSP00000348069|P36956|J3QLB6&B5MD58|UPI00004432F6|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000395751|nonsense_mediated_decay||10/17||||||||||-1||HGNC|11289|||||ENSP00000379100||J3QLB6|UPI000268B05F|||||||||||||,insertion|intron_variant&NMD_transcript_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000395756|nonsense_mediated_decay||6/13||||||||||-1|cds_start_NF|HGNC|11289|||||ENSP00000474121|||UPI00033350BF|||||||||||||,insertion|intron_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000395757|protein_coding||9/16||||||||||-1||HGNC|11289|||||ENSP00000379106||J3QLB6&B5MD58|UPI0000E59E65|||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000423161|protein_coding|||||||||||2837|-1|cds_end_NF|HGNC|11289|||||ENSP00000411516||J3QLB6&F6V242|UPI000268B061|||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000435530|protein_coding|||||||||||1376|-1||HGNC|11289|||||ENSP00000413389|P36956|J3QLB6|UPI0000200ABF|||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000447641|retained_intron||1/4||||||||||-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000469356|retained_intron|||||||||||335|-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000470247|retained_intron|||||||||||2033|-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000471445|retained_intron|||||||||||267|-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000476994|retained_intron|||||||||||3818|-1||HGNC|11289|||||||||||||||||||||,insertion|upstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000478616|protein_coding|||||||||||1834|-1|cds_start_NF|HGNC|11289|||||ENSP00000464923||K7EIW8|UPI0002840F4B|||||||||||||,insertion|upstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000485080|nonsense_mediated_decay|||||||||||2420|-1|cds_start_NF|HGNC|11289|||||ENSP00000466643||K7EMT8|UPI0002840F48|||||||||||||,insertion|upstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000486311|protein_coding|||||||||||1813|-1|cds_start_NF&cds_end_NF|HGNC|11289|||||ENSP00000466453||K7EMD1|UPI0002840F4A|||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000487401|retained_intron|||||||||||1336|-1||HGNC|11289|||||||||||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000490796|retained_intron||1/4||||||||||-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000577897|protein_coding|||||||||||2931|-1|cds_end_NF|HGNC|11289|||||ENSP00000463474||J3QLB6|UPI000268B063|||||||||||||,insertion|upstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000578469|nonsense_mediated_decay|||||||||||2747|-1|cds_start_NF|HGNC|11289|||||ENSP00000465747|||UPI0002840F49|||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000580540|retained_intron|||||||||||933|-1||HGNC|11289|||||||||||||||||||||,insertion|upstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000581707|retained_intron|||||||||||816|-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000583080|retained_intron|||||||||||1234|-1||HGNC|11289|||||||||||||||||||||,insertion|downstream_gene_variant|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000583732|processed_transcript|||||||||||2882|-1||HGNC|11289|||||||||||||||||||||,insertion|intron_variant&non_coding_transcript_variant&feature_elongation|MODIFIER|SREBF1|ENSG00000072310|Transcript|ENST00000584760|retained_intron||1/1||||||||||-1||HGNC|11289|||||||||||||||||||||:ENST00000261646:intron_variant&feature_elongation:ENST00000338854:intron_variant&feature_elongation:ENST00000355815:intron_variant&feature_elongation:ENST00000395751:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000395756:intron_variant&NMD_transcript_variant&feature_elongation:ENST00000395757:intron_variant&feature_elongation:ENST00000423161:downstream_gene_variant:ENST00000435530:downstream_gene_variant:ENST00000447641:intron_variant&non_coding_transcript_variant&feature_elongation:ENST00000469356:downstream_gene_variant:ENST00000470247:downstream_gene_variant:ENST00000471445:downstream_gene_variant:ENST00000476994:downstream_gene_variant:ENST00000478616:upstream_gene_variant:ENST00000485080:upstream_gene_variant:ENST00000486311:upstream_gene_variant:ENST00000487401:downstream_gene_variant:ENST00000490796:intron_variant&non_coding_transcript_variant&feature_elongation:ENST00000577897:downstream_gene_variant:ENST00000578469:upstream_gene_variant:ENST00000580540:downstream_gene_variant:ENST00000581707:upstream_gene_variant:ENST00000583080:downstream_gene_variant:ENST00000583732:downstream_gene_variant:ENST00000584760:intron_variant&non_coding_transcript_variant&feature_elongation;END=17719503;HOMLEN=11;HOMSEQ=CCCCCCAACCC;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=96;SVTYPE=INS;most_severe_consequence=11289:insertion|non_coding_transcript_variant GT:FT:GQ:PL:PR:SR 0/1:PASS:27:335,0,24:0,1:0,17 0/1:MinGQ:12:519,0,9:0,0:0,24 0/1:PASS:53:297,0,50:0,0:0,18
176
+ 20 54963149 MantaDUP:TANDEM:59:0:1:0:0:0 C <DUP:TANDEM> 340 PASS CSQ=duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000312783|protein_coding||3/9||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000321591|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000347343|protein_coding||2/8||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000216911|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000371356|protein_coding||3/9||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000360407|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000395907|protein_coding||2/7||||||||||-1||HGNC|11393|||||ENSP00000379243||Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1&A3KFJ0|UPI0000E5A34F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000395909|protein_coding||4/10||||||||||-1||HGNC|11393|YES|||CCDS13451.1|ENSP00000379245|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000395911|protein_coding||3/9||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000379247|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000395913|protein_coding||2/8||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000379249|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000395914|protein_coding||3/9||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000379250|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000395915|protein_coding||2/8||||||||||-1||HGNC|11393||||CCDS13451.1|ENSP00000379251|O14965|Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI000013C70F|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000420474|protein_coding||4/6||||||||||-1|cds_end_NF|HGNC|11393|||||ENSP00000388073||Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI0000470AC7|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000422322|protein_coding||3/5||||||||||-1|cds_end_NF|HGNC|11393|||||ENSP00000405042||Q5QPD2&Q5QPD1&A3KFJ2|UPI0000E5A34E|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000441357|protein_coding||3/7||||||||||-1|cds_end_NF|HGNC|11393|||||ENSP00000393452||Q5QPD4&Q5QPD2&Q5QPD1&A3KFJ2&A3KFJ1|UPI0000470AC5|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000451915|protein_coding||4/4||||||||||-1|cds_end_NF|HGNC|11393|||||ENSP00000401358||A3KFJ2|UPI0000E5A350|||||||||||||,duplication|intron_variant&feature_elongation|MODIFIER|AURKA|ENSG00000087586|Transcript|ENST00000456249|protein_coding||4/4||||||||||-1|cds_end_NF|HGNC|11393|||||ENSP00000405170||Q5QPD1&A3KFJ2|UPI0000470AC8|||||||||||||:ENST00000312783:intron_variant&feature_elongation:ENST00000347343:intron_variant&feature_elongation:ENST00000371356:intron_variant&feature_elongation:ENST00000395907:intron_variant&feature_elongation:ENST00000395909:intron_variant&feature_elongation:ENST00000395911:intron_variant&feature_elongation:ENST00000395913:intron_variant&feature_elongation:ENST00000395914:intron_variant&feature_elongation:ENST00000395915:intron_variant&feature_elongation:ENST00000420474:intron_variant&feature_elongation:ENST00000422322:intron_variant&feature_elongation:ENST00000441357:intron_variant&feature_elongation:ENST00000451915:intron_variant&feature_elongation:ENST00000456249:intron_variant&feature_elongation;END=54963210;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=61;SVTYPE=DUP;most_severe_consequence=11393:duplication|intron_variant GT:FT:GQ:PL:PR:SR 0/1:PASS:104:154,0,999:4,0:27,7 0/1:PASS:15:64,0,999:10,0:27,3 0/1:PASS:221:271,0,999:7,0:27,11
177
+ 21 46825202 MantaINS:65:0:0:0:0:1 G GCTGCGGGGCTGCGGGGGTCCCGGGGGTCCCGGGGGTCGGCTGGGTCCTGCGGGGGTC 999 PASS CIGAR=1M57I;CIPOS=0,8;CSQ=insertion|intron_variant&feature_elongation|MODIFIER|COL18A1|ENSG00000182871|Transcript|ENST00000400337|protein_coding||1/41||||||||||1||HGNC|2195||||CCDS42971.1|ENSP00000383191|P39060|D3DSM4|UPI0000207001|||||||||||||:ENST00000400337:intron_variant&feature_elongation;END=46825202;HOMLEN=8;HOMSEQ=CTGCGGGG;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=57;SVTYPE=INS;most_severe_consequence=2195:insertion|intron_variant GT:FT:GQ:PL:PR:SR 1/1:PASS:27:520,30,0:0,0:0,19 0/1:MinGQ:4:402,2,0:0,0:0,21 1/1:MinGQ:11:334,13,0:0,0:0,14
178
+ 21 46910447 MantaDEL:68:0:0:0:4:0 TGGGCCTCCGTGTGCCCTCCTGGGTCTCCGTGTGCCCTCTCAGGTCCCTGGGCCTCCGTGTGCCCTCCCGGGTCCCTGGGCCTTCGTGTGCCCTCCCAGGTCTCTGGGCCTCCGTGTGCCCACTCCCG T 618 PASS CIGAR=1M127D;CIPOS=0,1;CSQ=deletion|intron_variant&feature_truncation|MODIFIER|COL18A1|ENSG00000182871|Transcript|ENST00000342220|protein_coding||1/22||||||||||1|cds_start_NF|HGNC|2195|||||ENSP00000339118||H7BXV5|UPI0000E5A415|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|COL18A1|ENSG00000182871|Transcript|ENST00000355480|protein_coding||19/40||||||||||1||HGNC|2195|YES|||CCDS42972.1|ENSP00000347665|P39060|D3DSM5|UPI000016A19D|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|COL18A1|ENSG00000182871|Transcript|ENST00000359759|protein_coding||19/40||||||||||1||HGNC|2195|||||ENSP00000352798|P39060||UPI0001838820|||||||||||||,deletion|intron_variant&feature_truncation|MODIFIER|COL18A1|ENSG00000182871|Transcript|ENST00000400337|protein_coding||20/41||||||||||1||HGNC|2195||||CCDS42971.1|ENSP00000383191|P39060|D3DSM4|UPI0000207001|||||||||||||,deletion|upstream_gene_variant|MODIFIER|COL18A1|ENSG00000182871|Transcript|ENST00000459895|processed_transcript|||||||||||2535|1||HGNC|2195|||||||||||||||||||||:ENST00000342220:intron_variant&feature_truncation:ENST00000355480:intron_variant&feature_truncation:ENST00000359759:intron_variant&feature_truncation:ENST00000400337:intron_variant&feature_truncation:ENST00000459895:upstream_gene_variant;END=46910574;HOMLEN=1;HOMSEQ=G;RankResult=8|0|-12|1|3|0|4;RankScore=643594:4;SVLEN=-127;SVTYPE=DEL;most_severe_consequence=2195:deletion|intron_variant GT:FT:GQ:PL:PR:SR 0/1:PASS:260:310,0,421:2,2:13,14 0/1:PASS:195:245,0,275:0,1:6,9 0/1:PASS:88:213,0,85:0,1:3,10
tests/fixtures/test.vcf ADDED
@@ -0,0 +1,26 @@
1
+ ##fileformat=VCFv4.1
2
+ ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
3
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
4
+ ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
5
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6
+ ##contig=<ID=1,length=249250621,assembly=b37>
7
+ ##contig=<ID=10,length=135534747>
8
+ ##contig=<ID=X,length=155270560>
9
+ ##contig=<ID=MT,length=16569>
10
+ ##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
11
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father mother proband father_2 mother_2 proband_2
12
+ 1 879537 . T C 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 0/1:10,10:60 1/1:10,10:60 0/0:10,10:60 0/1:10,10:60 1/1:10,10:60
13
+ 1 879541 . G A 100 PASS MQ=1 GT:AD:GQ ./. 0/1:10,10:60 1/1:10,10:60 ./. 0/1:10,10:60 0/1:10,10:60
14
+ 1 879595 . C T 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 0/0:10,10:60 1/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60
15
+ 1 879676 . G A 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 1/1:10,10:60 1/1:10,10:60 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60
16
+ 1 879911 . G A 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60
17
+ 1 880012 . A G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60
18
+ 1 880086 . T C 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
19
+ 1 880199 . G A 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
20
+ 1 880217 . T G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
21
+ 10 76154051 . A G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60
22
+ 10 76154073 . T G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
23
+ 10 76154074 . C G 100 PASS MQ=1 GT:AD:GQ ./. 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60
24
+ 10 76154076 . G C 100 PASS MQ=1 GT:AD:GQ ./. 0/0:10,10:60 0/1:10,10:60 ./. 0/0:10,10:60 0/1:10,10:60
25
+ X 302253 . CCCTCCTGCCCCT C 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 1/1:10,10:60 0/0:10,10:60 1/1:10,10:60 1/1:10,10:60
26
+ MT 302253 . CCCTCCTGCCCCT C 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 1/1:10,10:60 0/0:10,10:60 1/1:10,10:60 1/1:10,10:60
tests/fixtures/test.vcf.gz ADDED
Binary file
tests/fixtures/test.vcf.gz.tbi ADDED
Binary file
tests/fixtures/unsorted.vcf ADDED
@@ -0,0 +1,20 @@
1
+ ##fileformat=VCFv4.1
2
+ ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
3
+ ##contig=<ID=1,length=249250621,assembly=b37>
4
+ ##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
5
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father mother proband father_2 mother_2 proband_2
6
+ 1 879537 . T C 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 0/1:10,10:60 1/1:10,10:60 0/0:10,10:60 0/1:10,10:60 1/1:10,10:60
7
+ 1 879541 . G A 100 PASS MQ=1 GT:AD:GQ ./. 0/1:10,10:60 1/1:10,10:60 ./. 0/1:10,10:60 0/1:10,10:60
8
+ 1 879595 . C T 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 0/0:10,10:60 1/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60
9
+ 1 879911 . G A 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60
10
+ 1 879676 . G A 100 PASS MQ=1 GT:AD:GQ 0/1:10,10:60 1/1:10,10:60 1/1:10,10:60 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60
11
+ 1 880012 . A G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60
12
+ 1 880086 . T C 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
13
+ 1 880199 . G A 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
14
+ 1 880217 . T G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
15
+ 10 76154051 . A G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60 0/0:10,10:60 0/1:10,10:60 0/1:10,10:60
16
+ 10 76154073 . T G 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60 0/0:10,10:60 0/0:10,10:60 0/1:10,10:60
17
+ 10 76154074 . C G 100 PASS MQ=1 GT:AD:GQ ./. 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60 0/1:10,10:60
18
+ 10 76154076 . G C 100 PASS MQ=1 GT:AD:GQ ./. 0/0:10,10:60 0/1:10,10:60 ./. 0/0:10,10:60 0/1:10,10:60
19
+ X 302253 . CCCTCCTGCCCCT C 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 1/1:10,10:60 0/0:10,10:60 1/1:10,10:60 1/1:10,10:60
20
+ MT 302253 . CCCTCCTGCCCCT C 100 PASS MQ=1 GT:AD:GQ 0/0:10,10:60 0/1:10,10:60 1/1:10,10:60 0/0:10,10:60 1/1:10,10:60 1/1:10,10:60
tests/functional/test_cli.py ADDED
@@ -0,0 +1,213 @@
1
+ from click.testing import CliRunner
2
+
3
+ from loqusdb.commands.cli import cli as base_command
4
+ from loqusdb.exceptions import ProfileError
5
+
6
+
7
+ def test_base_command():
8
+ runner = CliRunner()
9
+ result = runner.invoke(base_command, [])
10
+
11
+ assert result.exit_code == 0
12
+
13
+
14
+ def test_load_command(vcf_path, ped_path, real_mongo_adapter, real_db_name):
15
+ ## GIVEN a vcf_path a ped_path and a empty database
16
+ assert sum([1 for case in real_mongo_adapter.cases()]) == 0
17
+ runner = CliRunner()
18
+ ## WHEN inserting a case via the CLI
19
+ command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-f", ped_path]
20
+ result = runner.invoke(base_command, command)
21
+ ## THEN assert that the cli exits without problems
22
+ assert result.exit_code == 0
23
+ ## THEN assert that the case was added
24
+ assert sum([1 for case in real_mongo_adapter.cases()]) == 1
25
+
26
+
27
+ def test_load_command_no_ped_case_id(vcf_path, case_id, real_mongo_adapter, real_db_name):
28
+ ## GIVEN a vcf_path a ped_path and a empty database
29
+ assert real_mongo_adapter.case({"case_id": case_id}) is None
30
+ runner = CliRunner()
31
+ ## WHEN inserting a case via the CLI
32
+ command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-c", case_id]
33
+ result = runner.invoke(base_command, command)
34
+ ## THEN assert that the cli exits without problems
35
+ assert result.exit_code == 0
36
+ ## THEN assert that the case was added
37
+ assert real_mongo_adapter.case({"case_id": case_id})
38
+
39
+
40
+ def test_load_command_no_ped(vcf_path, ped_path, real_mongo_adapter, real_db_name):
41
+ ## GIVEN a vcf_path a ped_path and a empty database
42
+ runner = CliRunner()
43
+ ## WHEN inserting a case via the CLI without a ped file
44
+ command = ["--database", real_db_name, "load", "--variant-file", vcf_path]
45
+ result = runner.invoke(base_command, command)
46
+
47
+ ## THEN assert that the cli exits with code 1
48
+ assert result.exit_code == 1
49
+
50
+
51
+ def test_load_command_check_profile(
52
+ zipped_vcf_path, ped_path, real_mongo_adapter, real_db_name, profile_vcf_path
53
+ ):
54
+ NEW_CASE_NAME = "other_case"
55
+ # Load profile variants
56
+ runner = CliRunner()
57
+ command = ["--database", real_db_name, "profile", "--load", "--variant-file", profile_vcf_path]
58
+ result = runner.invoke(base_command, command)
59
+
60
+ # WHEN load command with --check-profile flag
61
+ command = [
62
+ "--database",
63
+ real_db_name,
64
+ "load",
65
+ "--variant-file",
66
+ zipped_vcf_path,
67
+ "-f",
68
+ ped_path,
69
+ "--check-profile",
70
+ zipped_vcf_path,
71
+ ]
72
+ result = runner.invoke(base_command, command)
73
+ ## THEN assert that the cli exits without problems
74
+ assert result.exit_code == 0
75
+ ## THEN assert if field 'profile is found in the individual documents'
76
+ for case in real_mongo_adapter.cases():
77
+ for individual in case["individuals"]:
78
+ assert individual.get("profile")
79
+
80
+ ##WHEN load the same case (change case-id with -c option)
81
+ command = [
82
+ "--database",
83
+ real_db_name,
84
+ "load",
85
+ "--variant-file",
86
+ zipped_vcf_path,
87
+ "-f",
88
+ ped_path,
89
+ "--check-profile",
90
+ zipped_vcf_path,
91
+ "-c",
92
+ "other_case",
93
+ ]
94
+ result = runner.invoke(base_command, command)
95
+ ## THEN assert that exit_code is not 0 and error is raised
96
+ assert result.exit_code != 0
97
+ assert type(result.exception) == ProfileError
98
+
99
+ ##WHEN try to insert the same case without --check-profile flag (should work)
100
+ command = [
101
+ "--database",
102
+ real_db_name,
103
+ "load",
104
+ "--variant-file",
105
+ zipped_vcf_path,
106
+ "-f",
107
+ ped_path,
108
+ "-c",
109
+ NEW_CASE_NAME,
110
+ ]
111
+ result = runner.invoke(base_command, command)
112
+ ## THEN assert that exit_code is 0
113
+ assert result.exit_code == 0
114
+ ## THEN assert that no profile string is added to the individuals
115
+ for individual in real_mongo_adapter.case({"case_id": NEW_CASE_NAME})["individuals"]:
116
+ assert not individual.get("profile")
117
+
118
+
119
+ def test_load_profile_command(profile_vcf_path, real_mongo_adapter, real_db_name):
120
+ runner = CliRunner()
121
+
122
+ command = ["--database", real_db_name, "profile", "--load", "--variant-file", profile_vcf_path]
123
+ result = runner.invoke(base_command, command)
124
+
125
+ assert result.exit_code == 0
126
+ assert len(list(real_mongo_adapter.profile_variants())) > 0
127
+
128
+
129
+ def test_delete_command_family_file(vcf_path, ped_path, real_mongo_adapter, real_db_name):
130
+ ## GIVEN a vcf_path a ped_path and a empty database
131
+ runner = CliRunner()
132
+ assert sum([1 for case in real_mongo_adapter.cases()]) == 0
133
+
134
+ ## WHEN inserting a case via the CLI without a ped file
135
+ load_command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-f", ped_path]
136
+ result = runner.invoke(base_command, load_command)
137
+ ## THEN assert that the case was added
138
+ assert sum(1 for case in real_mongo_adapter.cases()) == 1
139
+
140
+ ## WHEN deleting the case a case via the CLI without a ped file
141
+ delete_command = ["--database", real_db_name, "delete", "-f", ped_path]
142
+ result = runner.invoke(base_command, delete_command)
143
+
144
+ ## THEN assert that the cli exits without problems
145
+ assert result.exit_code == 0
146
+ ## THEN assert that the case was deleted
147
+ assert sum(1 for case in real_mongo_adapter.cases()) == 0
148
+
149
+
150
+ def test_delete_command_case_id(vcf_path, case_id, real_mongo_adapter, real_db_name):
151
+ ## GIVEN a vcf_path a ped_path and a empty database
152
+ runner = CliRunner()
153
+ assert real_mongo_adapter.case({"case_id": case_id}) is None
154
+
155
+ ## WHEN inserting a case via the CLI without a ped file
156
+ load_command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-c", case_id]
157
+ result = runner.invoke(base_command, load_command)
158
+ ## THEN assert that the case was added
159
+ assert isinstance(real_mongo_adapter.case({"case_id": case_id}), dict)
160
+
161
+ ## WHEN deleting the case a case via the CLI without a ped file
162
+ delete_command = ["--database", real_db_name, "delete", "-c", case_id]
163
+ result = runner.invoke(base_command, delete_command)
164
+
165
+ ## THEN assert that the cli exits without problems
166
+ assert result.exit_code == 0
167
+ ## THEN assert that the case was deleted
168
+ assert real_mongo_adapter.case({"case_id": case_id}) is None
169
+
170
+
171
+ def test_cases_command_case_id(vcf_path, case_id, real_mongo_adapter, real_db_name):
172
+ ## GIVEN a vcf_path a ped_path and a empty database
173
+ runner = CliRunner()
174
+ assert real_mongo_adapter.case({"case_id": case_id}) is None
175
+
176
+ ## WHEN inserting a case via the CLI without a ped file
177
+ load_command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-c", case_id]
178
+ result = runner.invoke(base_command, load_command)
179
+ ## THEN assert that the case was added
180
+ assert isinstance(real_mongo_adapter.case({"case_id": case_id}), dict)
181
+
182
+ ## WHEN searching for the case with CLI
183
+ command = ["--database", real_db_name, "cases", "--case-id", case_id]
184
+ result = runner.invoke(base_command, command)
185
+
186
+ ## THEN assert that the cli exits without problems
187
+ assert result.exit_code == 0
188
+
189
+
190
+ def test_cases_command_non_existing(vcf_path, case_id, real_mongo_adapter, real_db_name):
191
+ ## GIVEN a vcf_path a ped_path and a empty database
192
+ runner = CliRunner()
193
+ assert real_mongo_adapter.case({"case_id": case_id}) is None
194
+
195
+ ## WHEN searching for a non existing case
196
+ command = ["--database", real_db_name, "cases", "--case-id", "hello"]
197
+ result = runner.invoke(base_command, command)
198
+
199
+ ## THEN assert that the exit is zero
200
+ assert result.exit_code == 0
201
+ # Exit code should be 0 even if there is no result returned
202
+
203
+
204
+ # def test_wipe_command(mongo_client, vcf_path, ped_path):
205
+ # runner = CliRunner()
206
+ #
207
+ # load_command = ['-c', 'mongomock://', '--database', 'test', 'load', vcf_path, '-f', ped_path]
208
+ # runner.invoke(base_command, load_command)
209
+ #
210
+ # wipe_command = ['-c', 'mongomock://', '--database', 'test', 'wipe', '--yes']
211
+ # result = runner.invoke(base_command, wipe_command)
212
+ #
213
+ # assert result.exit_code == 0