1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/somaticFilter.wdl
View File
| @@ -27,9 +27,9 @@ task somaticFilter { | |||
| java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf | |||
| # Merge SNP and INDEL | |||
| awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Somatic.filter.vcf | cat - ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf > ${sample}.VarScan.TN.Somatic.filter.vcf | |||
| awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Germline.filter.vcf | cat - ${sample}.VarScan.TN.INDEL.Germline.filter.vcf > ${sample}.VarScan.TN.Germline.filter.vcf | |||
| awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.LOH.filter.vcf | cat - ${sample}.VarScan.TN.INDEL.LOH.filter.vcf > ${sample}.VarScan.TN.LOH.filter.vcf | |||
| awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.TN.Somatic.filter.vcf | |||
| awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Germline.filter.vcf | cat ${sample}.VarScan.TN.INDEL.Germline.filter.vcf - > ${sample}.VarScan.TN.Germline.filter.vcf | |||
| awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.LOH.filter.vcf | cat ${sample}.VarScan.TN.INDEL.LOH.filter.vcf - > ${sample}.VarScan.TN.LOH.filter.vcf | |||
| >>> | |||
| runtime { | |||
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