Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Merging VCF files after HaplotypeCaller->VariantFiltration

thkitapcithkitapci Los AngelesMember

Hi,
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 ?

Thanks
Best Regards
Hamdi

Answers

  • Tiffany_at_BroadTiffany_at_Broad admin 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 ?

    Thanks!
    Hamdi

  • Tiffany_at_BroadTiffany_at_Broad admin 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.

Sign In or Register to comment.