STR annotation

Answers

• delangel Broad InstituteMember ✭✭

  November 2012 Accepted Answer

  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.

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• ambarrio Member ✭

  January 2014

  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

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• xiucz Member ✭

  May 2019

  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.

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• xiucz Member ✭

  June 2019 edited June 2019

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

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• bhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

  June 2019

  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?

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• bhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

  June 2019

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

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• xiucz Member ✭

  June 2019 edited June 2019

  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:

  

  ~/gatk-4.1.0.0/gatk Mutect2 \
  -R ~/database/hg19/gatk_bundle/ucsc.hg19.fasta \
  -I ~/sample.recalibrated.bam -tumor samplename \
  -L ~/exon.bed --interval-padding 250 \
  --germline-resource ~/af-only-gnomad.raw.sites.hg19.vcf.gz \
  --tmp-dir ~/tmpdir -O sample.vcf \
  -bamout sample.recalibrated.mt2.bam
  
  ~/gatk-4.1.0.0/gatk GetPileupSummaries \
  -I ~/sample.recalibrated.bam \
  -L ~/exon.bed --interval-padding 250 \
  -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

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• bhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

  June 2019

  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.

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