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#22 smCounter2: somatic variant calling and UMIs with Chang Xu
Manage episode 210835368 series 1537951
Content provided by Roman Cheplyaka. All podcast content including episodes, graphics, and podcast descriptions are uploaded and provided directly by Roman Cheplyaka or their podcast platform partner. If you believe someone is using your copyrighted work without your permission, you can follow the process outlined here https://player.fm/legal.
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
If you enjoyed this episode, please consider supporting the podcast on Patreon.
70 episodes
Share
Manage episode 210835368 series 1537951
Content provided by Roman Cheplyaka. All podcast content including episodes, graphics, and podcast descriptions are uploaded and provided directly by Roman Cheplyaka or their podcast platform partner. If you believe someone is using your copyrighted work without your permission, you can follow the process outlined here https://player.fm/legal.
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
If you enjoyed this episode, please consider supporting the podcast on Patreon.
70 episodes
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Similar to the bioinformatics chat
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…
continue reading
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…
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…
continue reading
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…
continue reading
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…
continue reading
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