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Specify vcf fileformat

After running gatk, I further process the VCF file using pyvcf, which only supports VCFv4.1. With gatk3.6, it gets confused by the ##FORMAT, Number=R setting, which is new in VCFv4.2.

Is there a way to 'downgrade' a VCF file to an earlier format, or to instruct the GATK to output a certain version of the VCF file format?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin
    No that's not possible, sorry. You should tell the pyvcf developers they need to upgrade to the 4.2 spec. It's already been out for quite awhile.

    What do you need to do with pyvcf? Maybe we can recommend a GATK way to do it, to keep you moving.
  • Redmar_van_den_BergRedmar_van_den_Berg ✭✭ Member ✭✭

    Thank you for your response. I can use variantsToTable as a work around, so I'm not stuck waiting for pyvcf to support 4.2

    I will also contact the developer of pyvcf about this issue. I know the specs are at https://github.com/samtools/hts-specs, are there other resources that could come in handy for developers (such as an example 4.2 vcf file with all options enabled)?

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    OK, glad to hear you're not stuck. I'm not aware of anything intended for developers beyond the VCF spec itself, I'm afraid.

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