how to filter a multi-sample VCF file based on 0/0 genotype numbers
I created one multi-sample VCF file using CNVcaller program. When I checked VCF file, realized that some variants only have one 0/1 or 1/1 genotype and rest of genotypes for other samples are as 0/0. Based on my knowledge, the 0/0 genotype indicates the absence of the variant in the target sample, so I intend to remove the variants in which sample with the 0/0 genotype are more than 50% of the total samples.
Do you think the idea of removing the mentioned options is correct? How can I do this?
1 answer
bcftools view -i '(COUNT(GT="ref")+COUNT(GT="mis")) < {insert-correct-number-here}' input.vcf
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link
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by
Pierre Lindenbaum
the number should be 5
yes
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Pierre Lindenbaum
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