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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!
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STR annotation

Best Answer
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delangel Broad Institute ✭✭
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.
Answers
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.
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
How was the STR flagged in the INFO column? Please see the igvshot, and the mutect2 tumoronly
output here.
Thank you.
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.
Hi, @bhanuGandham
Thank you for your reply.
Yes, my question is "why the tool flagged here an STR"? It seems that there is only one repeated allele.
Screenshot and commands:
Xiucz
Hi @xiucz
This is what the Mutect2 dev said:
Only the "slippage" filter (previously "str_contraction"), not the STR INFO, means that M2 rejects a variant. The STR INFO field applies for any indel of one or more units of a repeat, even if, as in this case, there are as few as two repeat units in the reference. M2 would never filter such a short "STR," however. Currently we don't filter for STRs smaller than 8 reference bases, and we don't necessarily filter larger ones. We are about to come out (within two months) with a much-improved polymerase slippage filter.