1 ändrade filer med 1 tillägg och 3 borttagningar
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tasks/bcftools.wdl
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| @@ -26,9 +26,7 @@ task bcftools { | |||
| #bcftools index FUSCCTNBC330_pon.vcf.gz | |||
| #bcftools index FUSCCTNBC467_pon.vcf.gz | |||
| 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 | |||
| touch panel_of_normal.vcf | |||
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