hyunminkang
commented
4 years ago demuxlet is using only known variant sites and somatic mutation is highly unlikely to overlap with those sites, so it will be safe to use it in my opinion. Ploidy changes might be an issue if there are very large amounts of CNVs across the genome, which may affect genotyping accuracy. In such a case, using freemuxlet might help.
Hyun.
Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu
On Thu, Apr 9, 2020 at 12:55 AM Stephanie Yahn notifications@github.com wrote:
I am trying to demultiplex tumor samples using genotype data from healthy cells, and demuxlet is calling the majority of my tumor cells doublets. I'm looking for any insight about whether somatic mutations in the tumor cells could be causing an issue (not enough overlap with genotype SNPs?). Most cells have > 50 SNPs, median around 200 SNPs. Can demuxlet output which SNPs were most informative for each donor?
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I am trying to demultiplex tumor samples using genotype data from healthy cells, and demuxlet is calling the majority of my tumor cells doublets. I'm looking for any insight about whether somatic mutations in the tumor cells could be causing an issue (not enough overlap with genotype SNPs?). Most cells have > 50 SNPs, median around 200 SNPs. Can demuxlet output which SNPs were most informative for each donor?