Entering edit mode
9 weeks ago
Cvlind • 0
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:
- Generate .pileup from .bam with SamTools
- Generate .copynumber from .pileup with VarScan
- Generate .seg from .copynumber with DNAcopy (R)
- 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?