Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

GATK VQSR tranches

golharamgolharam Member ✭✭✭

Hi all - I'm stumped and need your help. I'm following the GATK best practices for calling variants with HaplotypeCaller in GVCF mode. One of my samples is NA12878, among 119 others samples in my cohort. For some reason GATK is missing a bunch of variants in this sample that I can clearly see in IGV but are not listed in the VCF. I discovered that the variant is being filtered out..reason being VQSRTranchesSNP99.00to99.90. The genotype is homozygous variant, DP is 243, Qual is 524742.54 and its known in dbSNP. I suspect this is happening to other variants.

How do I adjust VQSR or how tranches are used and variants get placed in? I supposed I need to fine tune my parameters...but I would think something as obvious as this variant would pass Filtering.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    There should be a "culprit" annotation in there flagging the annotation with the worst scores, which may be responsible for the variant getting filtered. That's supposed to help you figure out what's wrong.

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭
    edited March 2015

    @golharam I noticed your interval being named VQSRTranchesSNP99.00to99.90. I just wanted to let you know, that the VQSR best practices for SNPs are:

    --ts_filter_level 99.5 \
    -mode SNP \

    According to the VR documentation the default --TStranche values are 100.0, 99.9, 99.0, and 90.0. Perhaps try to run VR again with higher granularity; i.e. by adding 99.5 to --TStranche?

    To save you a bit of time you can check the culprits in your .recal.gz file before you apply the recalibration.

    I hope you are able to avoid filtering out your true variant.

    Is this low coverage data by any chance? You might be better off using UnifiedGenotyper in this case?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Oh yeah, the culprits are in the recal file. And increased tranche granularity may help (you can specify as many as you want). @tommycarstensen to the rescue :)

Sign In or Register to comment.