ABSOLUTE for tumour purity with WES
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Entering edit mode
15 months ago
Cvlind • 0

Hello,

I have WES paired data (tumour and normal) from Illumina sequencing and I would like to obtain a purity score.

ABSOLUTE seemed perfect but I can't get it to work. Here's my workflow:

  1. Generate .pileup from .bam with SamTools
  2. Generate .copynumber from .pileup with VarScan
  3. Generate .seg from .copynumber with DNAcopy (R)
  4. Use ABSOLUTE (R)

I found a lot of posts out there, but a majority of them are still unanswered and quite old (this is the error I'm getting now and can't get rid of: WES samples failing ABSOLUTE)

It's quite old now and I was wondering if it's still in use today, or if not what are the best alternatives?

Thanks!

tumour-purity ABSOLUTE WES • 376 views
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