Question

vcf.gz file Modified

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3.8 years ago

sskimvd • 0

Hello The filter column in the vcf.gz file is all "." Is there a way to replace "." with "PASS"? Thank you.

ChIP-Seq • 510 views

ADD COMMENT • link updated 3.8 years ago by Pierre Lindenbaum 161k • written 3.8 years ago by sskimvd • 0

score 1 · Answer 1 · 2020-07-18

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Entering edit mode

3.8 years ago

Pierre Lindenbaum 161k

gunzip -c in.vcf.gz |  awk -F '\t' '/^#/ {print;next;} {OFS="\t";if($7==".") $7="PASS";print}'

ADD COMMENT • link 3.8 years ago by Pierre Lindenbaum 161k