Filter VCF file for variant alleles
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13 months ago

Hello everyone,

I am looking to filter my VCF file with multiple samples to keep those variants that vary with respect to the reference (i.e., not 0/0) in more than x samples. For example, if x is 10, I want to only keep SNPs that vary in more than 5 samples in my dataset. Thanks in advance

VCF bcftools vcftools • 664 views
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use a filtering expression https://samtools.github.io/bcftools/bcftools.html#expressions , something like;

bcftools view -i 'COUNT(GT="AR")+COUNT(GT="AA") >=3' 
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What have you tried? You've mentioned bcftools as a tag, have you read the manual?

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I've tried bcftools, which seems to be the closest I've got, but I can't find anything to do this. I have also found vcftools --max-non-ref-ac, which I think might be able to do this, but I am not really sure how to use it, and was wondering if anyone has any experience here. Thanks

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can't find anything to do this

It's in there. If you had looked a little deeper, you would have found - on your own - exactly what Pierre has pointed to below.

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