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tasks/bcftools.wdl
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| #for i in `ls *.gz`; do bcftools index $i -f; done | #for i in `ls *.gz`; do bcftools index $i -f; done | ||||
| #bcftools merge -m all -f PASS,. --force-samples *.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf | #bcftools merge -m all -f PASS,. --force-samples *.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf | ||||
| else | else | ||||
| touch panel_of_normal.vcf | |||||
| echo 1 | |||||
| #touch panel_of_normal.vcf | |||||
| fi | fi | ||||
| >>> | >>> | ||||
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