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

Question

[curious]

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

Answer 1

[Pierre Lindenbaum]

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

[curious]

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

[Pierre Lindenbaum]

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

[curious]

that was it thanks