Is it possible to use SelectVariant to get exact variants from another VCF?

Hi,

I'm trying to get specific variants from a VCF file. I'm using SelectVariants' '--concordance'. This option is outputting any variant in the same genome position without regards for the actual REF and ALTs fields. Is there a way to get the variants matching REF exactly and ALTs at least containing the ALT in the concordance file?

Thanks,
Carlos

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Carlos,

    This is the expected behavior; SelectVariants doesn't check that the alleles match, just the position.

    Is there a way to get the variants matching REF exactly

    This worries me a little -- are you trying to compare callsets that have different REF alleles at the same position? That would be a sign that there is a mismatch between the references used to call the variants.

    and ALTs at least containing the ALT in the concordance file?

    I think the way to do this would be to subset using --concordance, combine the resulting VCFs, then check for genotype concordance using JEXL expressions. But others may have more straightforward suggestions.

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