Multiple VCF filtering

Question

[deniselavezzari]

Hi!

I have a vcf with 20 samples and I want to remove from it the variants that are commons (with the same zygosity) to all samples. How can I do it?

Thanks

Answer 1

[Ram]

Use bcftools view with an exclude/include expression that operates on COUNT(GT="hom") as shown in the examples here: https://samtools.github.io/bcftools/bcftools.html#expressions

[deniselavezzari]

Thank you very much.

[Ram]

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