I tried this but it didn't work
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filter varaints from vcf sample based on their presence in N number of samples ?
Is there any command in vcftools / bcftools aur any other tool to separate variants based on their presence in N number of samples. E.g I have 20 samples in a merged vcf file. I want to separate variants present in a minimum of 15 samples.. ?
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Pierre Lindenbaum
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hafiz.talhamalik
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not tested.
bcftools view -i 'N_PASS(GT!="mis" && GT!="RR")>=15 ' input.vcf.gz
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