From b85a5133d129b7d61d5b91f5ee3758d7a182a7b7 Mon Sep 17 00:00:00 2001 From: Yuuki Galaxy Date: Wed, 14 Apr 2021 10:52:09 +0800 Subject: [PATCH] * fixed: tasks/fgi.wdl --- etc/gatk-wdl/fm2/tasks/fgi.wdl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/etc/gatk-wdl/fm2/tasks/fgi.wdl b/etc/gatk-wdl/fm2/tasks/fgi.wdl index 0ff2924ba..cf158f0a5 100644 --- a/etc/gatk-wdl/fm2/tasks/fgi.wdl +++ b/etc/gatk-wdl/fm2/tasks/fgi.wdl @@ -77,9 +77,9 @@ task callSNP { mkdir -p "~{outputPath}" bcftools mpileup --threads 6 ~{inputBam} -d 30000 -Q 30 -f ~{referenceFasta} -p -Ob \ -a FORMAT/AD,FORMAT/SCR,FORMAT/ADF,FORMAT/ADR \ - --ff UNMAP,SECONDARY,QCFAIL \ + --ff UNMAP,SECONDARY,QCFAIL -B \ -o ~{bcfFile} - bcftools call -Oz -A -m ~{bcfFile} -o ~{snp0File} + bcftools call -Oz -A -c -p 0.9 ~{bcfFile} -o ~{snp0File} bcftools index ~{snp0File} bcftools annotate -a ~{dbsnpVCF} ~{snp0File} -c ID --collapse all -R ~{SNPosFile} -Oz -o ~{snpFile} bcftools index ~{snpFile} @@ -87,6 +87,7 @@ task callSNP { bcftools query -f'%ID\t[%DP\t%QUAL\t%TGT]\t%CHROM:%POS\n' ~{snpFile} -o ~{outputPath + "/../snpG.txt"} perl ~{helperPl} ~{outputPath + "/snp0.txt"} > ~{outputPath + "/../snp.txt"} } + # See for `-c -p 0.9`. This fix low recalculated BaseQ next to INDEL. output { File outSNP0txt = outputPath + "/snp0.txt" -- 2.11.4.GIT