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commands.txt
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commands.txt
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This section lists command(s) run by hrDetect workflow
* Running hrDetect
```
set -euo pipefail
$BCFTOOLS_ROOT/bin/bcftools view -f '~{structuralQUALfilter}' ~{structuralVcfFile} >> ~{outputFileNamePrefix}.structural.PASS.vcf
awk '$1 !~ "#" {print}' ~{structuralVcfFile} | wc -l >~{outputFileNamePrefix}.structural.filteringReport.txt
awk '$1 !~ "#" {print}' ~{outputFileNamePrefix}.structural.PASS.vcf | wc -l >>~{outputFileNamePrefix}.structural.filteringReport.txt
```
```
set -euo pipefail
$BCFTOOLS_ROOT/bin/bcftools norm --multiallelics - --fasta-ref ~{genome} ~{difficultRegions} ~{smallsVcfFile} | \
$BCFTOOLS_ROOT/bin/bcftools filter -i "TYPE='~{smallType}'" | \
$BCFTOOLS_ROOT/bin/bcftools filter -e "~{QUALfilter}" | \
$BCFTOOLS_ROOT/bin/bcftools filter -i "(FORMAT/AD[0:1])/(FORMAT/AD[0:0]+FORMAT/AD[0:1]) >= ~{VAF}" >~{outputFileNamePrefix}.~{smallType}.VAF.vcf
bgzip ~{outputFileNamePrefix}.~{smallType}.VAF.vcf
tabix -p vcf ~{outputFileNamePrefix}.~{smallType}.VAF.vcf.gz
zcat ~{smallsVcfFile} | awk '$1 !~ "#" {print}' | wc -l >~{outputFileNamePrefix}.~{smallType}.filteringReport.txt
zcat ~{outputFileNamePrefix}.~{smallType}.VAF.vcf.gz | awk '$1 !~ "#" {print}' | wc -l >>~{outputFileNamePrefix}.~{smallType}.filteringReport.txt
```
```
set -euo pipefail
Rscript ~{sigtoolrScript} \
--sampleName ~{outputFileNamePrefix} \
--snvFile ~{snvVcfFiltered} \
--indelFile ~{indelVcfFiltered} \
--SVFile ~{SV_vcf_location} \
--LOHFile ~{lohSegFile} \
--bootstraps ~{sigtoolsBootstrap} \
--genomeVersion ~{genomeVersion} \
--indelCutoff ~{indelCutoff} \
--SVrefSigs ~{SVrefSigs} \
--SNVrefSigs ~{SNVrefSigs}