loqusdb 2.7.2__py3-none-any.whl → 2.7.8__py3-none-any.whl

tests/fixtures/test.SV.vcf

@@ -0,0 +1,178 @@
+##fileformat=VCFv4.2
+##ALT=<ID=BND,Description="Translocation Breakend">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
+##ALT=<ID=INS,Description="Insertion">
+##ALT=<ID=INV,Description="Inversion">
+##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">
+##FILTER=<ID=MinGQ,Description="GQ score is less than 15 (filter applied at sample level and record level if all samples are filtered)">
+##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20">
+##FILTER=<ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample.">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
+##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">
+##INFO=<ID=1000GAF,Number=.,Type=Float,Description="calculated field: 1000GAF">
+##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">
+##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
+##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">
+##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 '|'.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=GeneticModels,Number=.,Type=String,Description="':'-separated list of genetic models for this variant.">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
+##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">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
+##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
+##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">
+##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
+##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
+##INFO=<ID=ModelScore,Number=.,Type=String,Description="PHRED score for genotype models.">
+##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
+##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
+##INFO=<ID=RankResult,Number=.,Type=String,Description="variant_length|Variant_call_quality_filter|Inheritance_Models|Consequence|variant_type|Gene_intolerance_prediction|allele_frequency">
+##INFO=<ID=RankScore,Number=.,Type=String,Description="The rank score for this variant in this family. family_id:rank_score.">
+##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
+##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=left_1000GAF,Number=.,Type=String,Description="1000 genomes frequency SV left interval">
+##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">
+##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">
+##INFO=<ID=most_severe_consequence,Number=.,Type=String,Description="Most severe genomic consequence.">
+##INFO=<ID=right_1000GAF,Number=.,Type=String,Description="1000 genomes frequency SV right interval">
+##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">
+##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">
+##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence)
+##LoF_filter=Reason for LoF not being HC
+##LoF_flags=Possible warning flags for LoF
+##LoF_info=Info used for LoF annotation
+##LoFtool=LoFtool score for gene
+##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">
+##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
+##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
+##bcftools_annotateVersion=1.3.1+htslib-1.3.1
+##bcftools_concatCommand=concat -a /scratch/717374/643594-miptest_pmanta.vcf.gz
+##bcftools_concatVersion=1.3.1+htslib-1.3.1
+##bcftools_viewCommand=view -f PASS /scratch/717374/643594-miptest_sorted_md_brecal_comb_SV_vt.vcf
+##bcftools_viewVersion=1.3.1+htslib-1.3.1
+##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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+##fileDate=20161208
+##reference=file:///mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta
+##source=GenerateSVCandidates 1.0.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	father	proband	mother
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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

@@ -0,0 +1,26 @@
+##fileformat=VCFv4.1
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=1,length=249250621,assembly=b37>
+##contig=<ID=10,length=135534747>
+##contig=<ID=X,length=155270560>
+##contig=<ID=MT,length=16569>
+##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	father	mother	proband	father_2	mother_2	proband_2
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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/unsorted.vcf

@@ -0,0 +1,20 @@
+##fileformat=VCFv4.1
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##contig=<ID=1,length=249250621,assembly=b37>
+##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	father	mother	proband	father_2	mother_2	proband_2
+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
+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
+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
+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
+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
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tests/functional/test_cli.py

@@ -0,0 +1,213 @@
+from click.testing import CliRunner
+
+from loqusdb.commands.cli import cli as base_command
+from loqusdb.exceptions import ProfileError
+
+
+def test_base_command():
+    runner = CliRunner()
+    result = runner.invoke(base_command, [])
+
+    assert result.exit_code == 0
+
+
+def test_load_command(vcf_path, ped_path, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    assert sum([1 for case in real_mongo_adapter.cases()]) == 0
+    runner = CliRunner()
+    ## WHEN inserting a case via the CLI
+    command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-f", ped_path]
+    result = runner.invoke(base_command, command)
+    ## THEN assert that the cli exits without problems
+    assert result.exit_code == 0
+    ## THEN assert that the case was added
+    assert sum([1 for case in real_mongo_adapter.cases()]) == 1
+
+
+def test_load_command_no_ped_case_id(vcf_path, case_id, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    assert real_mongo_adapter.case({"case_id": case_id}) is None
+    runner = CliRunner()
+    ## WHEN inserting a case via the CLI
+    command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-c", case_id]
+    result = runner.invoke(base_command, command)
+    ## THEN assert that the cli exits without problems
+    assert result.exit_code == 0
+    ## THEN assert that the case was added
+    assert real_mongo_adapter.case({"case_id": case_id})
+
+
+def test_load_command_no_ped(vcf_path, ped_path, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    runner = CliRunner()
+    ## WHEN inserting a case via the CLI without a ped file
+    command = ["--database", real_db_name, "load", "--variant-file", vcf_path]
+    result = runner.invoke(base_command, command)
+
+    ## THEN assert that the cli exits with code 1
+    assert result.exit_code == 1
+
+
+def test_load_command_check_profile(
+    zipped_vcf_path, ped_path, real_mongo_adapter, real_db_name, profile_vcf_path
+):
+    NEW_CASE_NAME = "other_case"
+    # Load profile variants
+    runner = CliRunner()
+    command = ["--database", real_db_name, "profile", "--load", "--variant-file", profile_vcf_path]
+    result = runner.invoke(base_command, command)
+
+    # WHEN load command with --check-profile flag
+    command = [
+        "--database",
+        real_db_name,
+        "load",
+        "--variant-file",
+        zipped_vcf_path,
+        "-f",
+        ped_path,
+        "--check-profile",
+        zipped_vcf_path,
+    ]
+    result = runner.invoke(base_command, command)
+    ## THEN assert that the cli exits without problems
+    assert result.exit_code == 0
+    ## THEN assert if field 'profile is found in the individual documents'
+    for case in real_mongo_adapter.cases():
+        for individual in case["individuals"]:
+            assert individual.get("profile")
+
+    ##WHEN load the same case (change case-id with -c option)
+    command = [
+        "--database",
+        real_db_name,
+        "load",
+        "--variant-file",
+        zipped_vcf_path,
+        "-f",
+        ped_path,
+        "--check-profile",
+        zipped_vcf_path,
+        "-c",
+        "other_case",
+    ]
+    result = runner.invoke(base_command, command)
+    ## THEN assert that exit_code is not 0 and error is raised
+    assert result.exit_code != 0
+    assert type(result.exception) == ProfileError
+
+    ##WHEN try to insert the same case without --check-profile flag (should work)
+    command = [
+        "--database",
+        real_db_name,
+        "load",
+        "--variant-file",
+        zipped_vcf_path,
+        "-f",
+        ped_path,
+        "-c",
+        NEW_CASE_NAME,
+    ]
+    result = runner.invoke(base_command, command)
+    ## THEN assert that exit_code is 0
+    assert result.exit_code == 0
+    ## THEN assert that no profile string is added to the individuals
+    for individual in real_mongo_adapter.case({"case_id": NEW_CASE_NAME})["individuals"]:
+        assert not individual.get("profile")
+
+
+def test_load_profile_command(profile_vcf_path, real_mongo_adapter, real_db_name):
+    runner = CliRunner()
+
+    command = ["--database", real_db_name, "profile", "--load", "--variant-file", profile_vcf_path]
+    result = runner.invoke(base_command, command)
+
+    assert result.exit_code == 0
+    assert len(list(real_mongo_adapter.profile_variants())) > 0
+
+
+def test_delete_command_family_file(vcf_path, ped_path, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    runner = CliRunner()
+    assert sum([1 for case in real_mongo_adapter.cases()]) == 0
+
+    ## WHEN inserting a case via the CLI without a ped file
+    load_command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-f", ped_path]
+    result = runner.invoke(base_command, load_command)
+    ## THEN assert that the case was added
+    assert sum(1 for case in real_mongo_adapter.cases()) == 1
+
+    ## WHEN deleting the case a case via the CLI without a ped file
+    delete_command = ["--database", real_db_name, "delete", "-f", ped_path]
+    result = runner.invoke(base_command, delete_command)
+
+    ## THEN assert that the cli exits without problems
+    assert result.exit_code == 0
+    ## THEN assert that the case was deleted
+    assert sum(1 for case in real_mongo_adapter.cases()) == 0
+
+
+def test_delete_command_case_id(vcf_path, case_id, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    runner = CliRunner()
+    assert real_mongo_adapter.case({"case_id": case_id}) is None
+
+    ## WHEN inserting a case via the CLI without a ped file
+    load_command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-c", case_id]
+    result = runner.invoke(base_command, load_command)
+    ## THEN assert that the case was added
+    assert isinstance(real_mongo_adapter.case({"case_id": case_id}), dict)
+
+    ## WHEN deleting the case a case via the CLI without a ped file
+    delete_command = ["--database", real_db_name, "delete", "-c", case_id]
+    result = runner.invoke(base_command, delete_command)
+
+    ## THEN assert that the cli exits without problems
+    assert result.exit_code == 0
+    ## THEN assert that the case was deleted
+    assert real_mongo_adapter.case({"case_id": case_id}) is None
+
+
+def test_cases_command_case_id(vcf_path, case_id, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    runner = CliRunner()
+    assert real_mongo_adapter.case({"case_id": case_id}) is None
+
+    ## WHEN inserting a case via the CLI without a ped file
+    load_command = ["--database", real_db_name, "load", "--variant-file", vcf_path, "-c", case_id]
+    result = runner.invoke(base_command, load_command)
+    ## THEN assert that the case was added
+    assert isinstance(real_mongo_adapter.case({"case_id": case_id}), dict)
+
+    ## WHEN searching for the case with CLI
+    command = ["--database", real_db_name, "cases", "--case-id", case_id]
+    result = runner.invoke(base_command, command)
+
+    ## THEN assert that the cli exits without problems
+    assert result.exit_code == 0
+
+
+def test_cases_command_non_existing(vcf_path, case_id, real_mongo_adapter, real_db_name):
+    ## GIVEN a vcf_path a ped_path and a empty database
+    runner = CliRunner()
+    assert real_mongo_adapter.case({"case_id": case_id}) is None
+
+    ## WHEN searching for a non existing case
+    command = ["--database", real_db_name, "cases", "--case-id", "hello"]
+    result = runner.invoke(base_command, command)
+
+    ## THEN assert that the exit is zero
+    assert result.exit_code == 0
+    # Exit code should be 0 even if there is no result returned
+
+
+# def test_wipe_command(mongo_client, vcf_path, ped_path):
+#     runner = CliRunner()
+#
+#     load_command = ['-c', 'mongomock://', '--database', 'test', 'load', vcf_path, '-f', ped_path]
+#     runner.invoke(base_command, load_command)
+#
+#     wipe_command = ['-c', 'mongomock://', '--database', 'test', 'wipe', '--yes']
+#     result = runner.invoke(base_command, wipe_command)
+#
+#     assert result.exit_code == 0