quick way to get samples that are NOT homozygous reference for a given record using bcftools?
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16 days ago
curious ▴ 520

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 • 236 views
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16 days ago
 bcftools view -i 'count(GT=="RR")==0' 
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[filter.c:1379 filters_init1] Error: the tag "INFO/count" is not defined in the VCF header ?

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

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that was it thanks

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