the bioinformatics chat

#22 smCounter2: somatic variant calling and UMIs with Chang Xu

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In this episode I’m joined by Chang Xu. Chang is a senior biostatistician

at QIAGEN and an author of smCounter2, a low-frequency somatic variant caller.
To distinguish rare somatic mutations from sequencing errors, smCounter2
relies on unique molecular identifiers, or UMIs, which help identify multiple
reads resulting from the same physical DNA fragment.

Chang explains what UMIs are, why they are useful, and how smCounter2 and other

tools in this space use UMIs to detect low-frequency variants.

Links:

  • smCounter2 preprint
  • smCounter2 github repository
  • smCounter publication
  • Review of somatic SNV callers

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    the bioinformatics chatBy Roman Cheplyaka
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