Mutect2: STR flag from INFO Field is not applied to multiallelic sites

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mack812

• February 11, 2020 11:37
• Edited

Hi,
 
I find the STR flag in the vcf file generated by M2 really useful when working with certain variants and applications (i.e. knowing that the variant under study is located at a microsatellite is a valuable piece of information in several ways). I am referring to the field with the following entry in the vcf header:

```
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
```

Also other associated fields such as RPA, RU or STRQ are useful. However, I have found that the STR flag is never applied to multiallelic sites like the one shown below:

- The following is a vcf entry of a multiallelic variant located at chr17 41246531 (GRCh37). It involves an indel and a SNV (this is usually the situation that I am seeing when the flag is not applied). The STR flag was not applied despite one of the variants (the DEL) being on a T[7] mononucleotide stretch in the ref. genome:

```
chr17 41246531 . CT C,TT . .
DP=4587;ECNT=30;MBQ=23,23,25;MFRL=0,0,0;MMQ=91,82,86;MPOS=13,17;OCM=0;POPAF=2.40,2.40;TLOD=1104.37,1.03
GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:3642,908,24:0.174,2.457e-03:4574:1533,492,0:1253,81,13:2017,1625,310,622
```

I know that multiallelic variants are messy but since microsatellite sites are particularly prone to multiallelic variants (i.e. highly polymorphic in the population, prone to somatic change in length in tumors, or are artefactually produced by DNA polymerase slippage and/or homopolymer error in some particular single-nucleotide addition seq. technologies), I wonder if it would be possible to apply the STR flag and related fields also to multiallelic sites in upcoming releases of GATK.
 
Thanks

0

• 

  Tiffany Miller

  • February 26, 2020 14:23
  • Edited

  Hi mack812 ! Our team is actually working on this now (it is under code review) and it should be merged soon! I'll see if I can get a github ticket id that you can follow. 

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  mack812

  • February 25, 2020 08:38
  • Edited

  Hi Tiffany Miller,

  OK, great! And thanks for the info.

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  Tiffany Miller

  • February 26, 2020 14:25

  The ticket appears to be on a private repo right now - sorry about that. 

  But it should be included in one of the next few releases!

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  mack812

  • February 27, 2020 09:44

  Hi Tiffany Miller,

  That's fine. I will keep an eye on upcoming releases. Thanks again for your help.

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