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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-4.1.0.0/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!

Answers

  • 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?

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