mutations_caller_pipeline_aws 0.0.9 → 0.0.10
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.
|
@@ -8,7 +8,7 @@ class BwaCaller
|
|
|
8
8
|
end
|
|
9
9
|
|
|
10
10
|
def self.call_paired_end(r1, r2, out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
|
|
11
|
-
cmd = "qsub -cwd -b y -N bwa_#{job_prefix} -l h_vmem=9G -pe make 4 #{account}\
|
|
11
|
+
cmd = "qsub -V -cwd -b y -N bwa_#{job_prefix} -l h_vmem=9G -pe make 4 #{account}\
|
|
12
12
|
#{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
|
|
13
13
|
<(#{bwa} aln #{index} #{r1} 2>>#{log_file}) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
|
|
14
14
|
#{r1} #{r2} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"
|
|
@@ -3,7 +3,7 @@ class GatkCaller
|
|
|
3
3
|
# Genotyper
|
|
4
4
|
def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account, debug)
|
|
5
5
|
cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
|
|
6
|
-
qsub -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=3G -hold_jid recalibration_#{job_prefix} #{account}\
|
|
6
|
+
qsub -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=3G -hold_jid recalibration_#{job_prefix} #{account}\
|
|
7
7
|
#{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
|
|
8
8
|
-I #{read_bam} \
|
|
9
9
|
-o #{read_vcf} \
|
|
@@ -16,7 +16,7 @@ class GatkCaller
|
|
|
16
16
|
# Making recalibration table
|
|
17
17
|
def self.recalibrate_bam(log_dir ,gatk, index_fa, index_vcf, read_bam, recal_file, job_prefix, account, debug )
|
|
18
18
|
cmd = "echo 'starting recalibration table ' `date` >> #{log_dir}
|
|
19
|
-
qsub -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=4G -hold_jid realignment_#{job_prefix} #{account} \
|
|
19
|
+
qsub -V -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=4G -hold_jid realignment_#{job_prefix} #{account} \
|
|
20
20
|
#{gatk} -knownSites #{index_vcf} -I #{read_bam} \
|
|
21
21
|
-R #{index_fa} -T CountCovariates \
|
|
22
22
|
-cov ReadGroupCovariate -cov QualityScoreCovariate -cov DinucCovariate \
|
|
@@ -29,7 +29,7 @@ class GatkCaller
|
|
|
29
29
|
# Using recalibration table
|
|
30
30
|
def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug)
|
|
31
31
|
cmd = "echo 'recalibrating bam_file at ' `date` >> #{log_dir}
|
|
32
|
-
qsub -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=4G -hold_jid recalibration_table_#{job_prefix} #{account} \
|
|
32
|
+
qsub -V -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=4G -hold_jid recalibration_table_#{job_prefix} #{account} \
|
|
33
33
|
#{gatk} \
|
|
34
34
|
-R #{index_fa} \
|
|
35
35
|
-I #{read_bam} \
|
|
@@ -43,7 +43,7 @@ class GatkCaller
|
|
|
43
43
|
# Preparation realignement
|
|
44
44
|
def self.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals, job_prefix, account, debug)
|
|
45
45
|
cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
|
|
46
|
-
qsub -cwd -b y -N prep_realignment_#{job_prefix} -l h_vmem=4G -hold_jid indexing_#{job_prefix} #{account}\
|
|
46
|
+
qsub -V -cwd -b y -N prep_realignment_#{job_prefix} -l h_vmem=4G -hold_jid indexing_#{job_prefix} #{account}\
|
|
47
47
|
#{gatk} \
|
|
48
48
|
-I #{read_bam} \
|
|
49
49
|
-R #{index_fa} \
|
|
@@ -56,7 +56,7 @@ class GatkCaller
|
|
|
56
56
|
# Realignment
|
|
57
57
|
def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug)
|
|
58
58
|
cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
|
|
59
|
-
qsub -cwd -b y -N realignment_#{job_prefix} -l h_vmem=4G -hold_jid prep_realignment_#{job_prefix} #{account} \
|
|
59
|
+
qsub -V -cwd -b y -N realignment_#{job_prefix} -l h_vmem=4G -hold_jid prep_realignment_#{job_prefix} #{account} \
|
|
60
60
|
#{gatk} \
|
|
61
61
|
-I #{read_bam} \
|
|
62
62
|
-R #{index_fa} \
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
class SamtoolsIndexing
|
|
2
2
|
def self.call(bam_file, job_prefix, account, debug)
|
|
3
|
-
cmd = "qsub -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
|
|
3
|
+
cmd = "qsub -V -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
|
|
4
4
|
samtools index #{bam_file}"
|
|
5
5
|
puts cmd
|
|
6
6
|
system(cmd) if debug == 1
|