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tasks/bcftools.wdl
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| for i in ${sep=" " vcf} | for i in ${sep=" " vcf} | ||||
| do | do | ||||
| echo "Processing:" $i | |||||
| bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz) --threads $nt | bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz) --threads $nt | ||||
| bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f --threads $nt | bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f --threads $nt | ||||
| done | done | ||||
| echo "Start bcftools merge ..." | |||||
| bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz --threads $nt | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf | bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz --threads $nt | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf | ||||
| >>> | >>> | ||||
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