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Force output of certain regions in GenotypeGVCFs

APredeusAPredeus Saint Petersburg, RussiaMember

Hello all,

It is a described problem that when you get your calls in the form of VCF file after GenotypeGVCFs, some of the medically relevant variants may be missing and it's impossible to tell whether they are not reported due to the position being a homozygous reference, or due to low coverage or another sequencing issue.

Is there an option to force certain regions to be output, e.g. from an external BED file etc? Would such an option be a useful addition to this tool?

Thank you in advance.

Best Answer


  • APredeusAPredeus Saint Petersburg, RussiaMember

    Hello again,

    just wanted to make sure the question is not overlooked. Any input would be appreciated - e.g. if you think this option would not be useful, etc. Also would be happy to answer any questions.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi, this can already be done using a combination of -allSites and -L, which can take an interval list, bed or vcf file.

  • APredeusAPredeus Saint Petersburg, RussiaMember

    Dear Geraldine, thank you for your answer, and sorry for getting back to you so late.

    The options you suggest would result in the forced output of the interval list variants ONLY.

    What I was looking for, however, is a normal filtered VCF PLUS the forced regions of interest.

    I understand that this could be done by running the program twice and then integrating the VCF files, but it seems that a singular option would be more streamlined. We'd consider a pull request into the development version if that is possible.

    Thank you in advance.

  • SheilaSheila Broad InstituteMember, Broadie admin


    I think using -allSites as Geraldine suggested above will give you what you want.


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