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ignore contig lines from the VCF output

Hi GATK team:

is there a flag that I can turn so that the VCF output will not contain the ##contig lines? I'm using VariantsToVCF. I tried SelectHeaders as well but it doesn't help.

Best Regards,

Jerry

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No, there isn't. Any particular reason you need to get rid of them?

  • jerrylamjerrylam Member

    Hi Geraldine:

    According to the specification, it is recommended but not necessary to have those contig lines. It seems a bit overkill to output all contig lines ing the intermediate steps of processing.

    Since, the SelectHeaders actually allows to remove INFO, FILTER, etc headerlines (those are required), it makes sense to allow users to select to exclude contig lines from the output.

    Best Regards,

    Jerry

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Fair point. At the moment we don't have the bandwidth to add that capability, but if you were to implement it we'd be happy to look at a patch.

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