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Picard SortVcf changing VCF file version

I am using Picard SortVcf to reorder the order to match the order of my reference genome and BAM files. And it works great, however it seems to be changing the VCF format from 4.0 to 4.2, and this is incompatible with the downstream steps I need it for. Is there any workaround for this?

Thanks!

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  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @cascott
    Hi,

    Is this happening with the latest Picard version? What downstream steps are incompatible with version 4.2?

    Thanks,
    Sheila

  • Hi,

    Sorry for the late reply. It is happening with the latest picard. It it at least changing the vcf file header to "##fileformat=VCFv4.2" even when the input vcf is a 4.0 or 4.1.

    The downstream tool that it is incompatible with is BisSNP, which development on has seemed to come to a halt.

    Thanks for your help!
    Anthony

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