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.
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.

# STR annotation

Member

May I know how is this defined?

If STR is present in the INFO field, then indel is a tandem repeat. If present, then annotation RU gives a string representing the bases that form the repeat unit, and RPA are the repeats per allele.
For example, if a (CA)^3 becomes (CA)^4 (2 bp insertion), then STR is present, RU = CA, and RPA = 3,4.

If STR is present in the INFO field, then indel is a tandem repeat. If present, then annotation RU gives a string representing the bases that form the repeat unit, and RPA are the repeats per allele.
For example, if a (CA)^3 becomes (CA)^4 (2 bp insertion), then STR is present, RU = CA, and RPA = 3,4.

• Member

Dear @delangel,

I wonder then, if I get a lot of negative values, is this because of STRs that are deletions to the reference genome?

Best

• Member

How was the STR flagged in the INFO column? Please see the igvshot, and the mutect2 tumoronly
output here.

```chrX    15349851    .   TA  T   .   PASS    CONTQ=93;DP=26;ECNT=1;GERMQ=18;MBQ=35,36;MFRL=256,222;MMQ=60,60;MPOS=40;POPAF=7.30;RPA=2,1;RU=A;SAAF=0.283,0.273,0.308;SAPP=0.017,0.026,0.957;STR;TLOD=22.22    GT:AD:AF:DP:F1R2:F2R1:OBAM:OBAMRC   0/1:18,8:0.321:26:9,3:9,5:false:false
```

Thank you.

• Member
edited June 3

Any GATKers can give me some suggestions ?
Thank you very much.

Hi @xiucz

Apologies for the delay in replying. In order to clarify, is your question "why the tool flagged this an STR"? Could you also provide a bam and bamout screenshots of this region to compare?

Also please post the version of Mutect2 used and the exact command.

• Member
edited June 11

Yes, my question is "why the tool flagged here an STR"? It seems that there is only one repeated allele.
Screenshot and commands:

```~/gatk-4.1.0.0/gatk Mutect2 \
-R ~/database/hg19/gatk_bundle/ucsc.hg19.fasta \
-I ~/sample.recalibrated.bam -tumor samplename \
--tmp-dir ~/tmpdir -O sample.vcf \
-bamout sample.recalibrated.mt2.bam

~/gatk-4.1.0.0/gatk GetPileupSummaries \
-I ~/sample.recalibrated.bam \
-V ~/small_exac_common_3_hg19.vcf.gz \
-O sample.tumor.getpileupsummaries.table

~/gatktools/gatk-4.1.0.0/gatk CalculateContamination \
-I sample.tumor.getpileupsummaries.table \
-O sample.calculatecontamination.table

~/gatk-4.1.0.0/gatk FilterMutectCalls \
-V sample.vcf \
--contamination-table sample.calculatecontamination.table \
-O sampple.mutect2_oncefilter.vcf
```

Xiucz