VCF filtering

0

Hi everyone,

I have a multisample VCF file (30 samples) with haploid calls and I want to filter off all sites where this condition holds true;

'sum of ref (GT=0) and missing/uncalled ( GT=".") genotypes in all samples is 30'

I have tried this in bcftools but it doesn't seem to work ;

bcftools view -e '(sum(GT[] =".") + sum(GT[]="0")) == 30' samples.vcf > filtered_samples.vcf

Please advise on how to correctly do it with bcftools or with any other approach.

Thanks!


vcf


SNPfiltering


genotype

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