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Merging VCF files after HaplotypeCaller->VariantFiltration

thkitapcithkitapci Los AngelesMember

I have a RNA dataset that I am calling variants (10 sample). After running gatk4 on all samples independently I want to merge the resulting VCF files for the downstream analysis that requires a multi sample VCF file. I tried to use vcf-merge and bcftools I realize that the INFO field of only one sample is included in the merged file.

How can I merge VCF files without loosing any information about samples ?

Best Regards


  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin
  • bramblepussbramblepuss Member
    I have to "be around for a little while longer" before I can post links, but there are two pages/posts that may help you if you search for these titles:

    1) My previous forum post, titled, "Correct GATK4 tools to use for combining scattered gVCFS and VCFs from multiple calls" - discussion 5653.

    2) A post by delangel of Broad, titled, "Combining variants from different files into one" - discussion 53.

    As Tiffany suggests, you can use CombineVariants from GATK3 to achieve this.
  • thkitapcithkitapci Los AngelesMember

    Hi Tiffany and bramblepuss,

    Thanks for your replies and thanks for the links to other posts.

    It seems CombineVariants should work for me. I have generated my VCF files with GATK4 can I use CombineVariants from GATK3 to combine VCF files generated with GATK4 ?


  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Yes, this should be fine @thkitapci
    You could see if GatherVCFs from GATK4 will work, but I've seen folks report that it cannot concatenate unsorted VCFs or merge different INFO fields correctly.

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