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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

A missing deletion in the tri-nucleotide repeat sequence using GATK-Mutect2 (v4.1.0.0)

Hi GATK team,

I performed whole-exome seq, followed by variant calling by GATK-Mutec2 (v4.1.0.0). I found there is a deletion occurred in input Bam and bamout file in my two samples, however, the Mutect2 did not call this variant in VCF. The allele frequency (AF) of such deletion in the one sample is 6.0% and 7.0% in the input BAM and Bamout, respectively. Please see the figure attached.

Interestingly, this tri-nucleotides deletion (GAG; chr4:88,929,174-88,929,176) occurs at the begging of GAG repeats (6x repeats). Therefore, I’d like to ask if there’s any reason that Mutect2 could not call the deletion in the repetitive sequence?

The following is the command for GATK-Mutect2,
date; /GATK/gatk- --java-options "-Xmx256g" Mutect2
-R /reference/hg19_forGATK_sinica.fa
-I /BAM/19030211_F0x100.bam
-tumor 19030211
-O /VCF/19030211_F0x100_Mutect2_tumor_maxaf1_mrra0.vcf.gz
-bamout 19030211_bamout.bam
--max-population-af 1
--max-reads-per-alignment-start 0 ;date

Your advise is highly appreciated, and look forward to your reply.

Thank you!


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Yenan

    I checked with the developer and this is what he said:
    While the bamout shows 22 deletions they are not all the same deletion and therefore none have sufficient evidence to be called. This is common in STRs, where you might have a few reads with a 1-unit deletion, a few with 2-unit deletions etc. In order to better determine what is going on we need i) the bamout sorted by base so we can see all deletion reads and ii) the vcf from running M2 with -emit-lod -1 at this locus.

    Also, why are you using neither a pon (our hg19 exome pon is public) nor the gnomad germline resource?

Sign In or Register to comment.