Question

quick way to get samples that are NOT homozygous reference for a given record using bcftools?

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3.7 years ago

curious ▴ 820

I can do this in python, but just wondered if there is any way in bcftools to return a vcf with samples that are NOT homozygous reference for a given snp. I am guessing no, but thought I would ask anyways

bcftools • 1.4k views

ADD COMMENT • link 3.7 years ago by curious ▴ 820

GenoMax · Answer 1 · 2021-04-21

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3.7 years ago

Pierre Lindenbaum 164k

 bcftools view -i 'count(GT=="RR")==0'

ADD COMMENT • link updated 3.7 years ago by GenoMax 148k • written 3.7 years ago by Pierre Lindenbaum 164k

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[filter.c:1379 filters_init1] Error: the tag "INFO/count" is not defined in the VCF header ?

ADD REPLY • link 3.7 years ago by curious ▴ 820

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what is your version of bcftools ? check you're using a recent version.

ADD REPLY • link 3.7 years ago by Pierre Lindenbaum 164k

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that was it thanks

ADD REPLY • link 3.7 years ago by curious ▴ 820