Pipeline which take care of tumor-normal contamination to correlate VAF, CNA and mRNA expression (WGS, RNASeq)
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3.4 years ago

Is there any way to correlate VAF information with bulk-transcriptome expression after adjustment of purity and ploidy of the cancer samples? e.g., in one of the samples, I found that the VAF is 0.17, and the copy number of the samples is ~5 (after adjustment of purity and ploidy by the purple tool). Purple can adjust the variant copy number. But it seems very challenging how to correlate it with the bulk-RNA expression. Any suggestions for the best tool which can take care of tumor purity adjustment for mRNA expression from RNAseq?

RNA-Seq whole genome sequencing SNV next-gen CNA • 853 views

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