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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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Purity values NA and suggestions? #204

Open jiwonhong95 opened 3 days ago

jiwonhong95 commented 3 days ago

Hi,

I'm trying to analyze tumor purity using facets and came across some issues where purity value is NA. Analyzing 150 samples, 24 were NA so its an issue that occurs too frequently to be ignored, and I've noticed there were quite a few others also dealing with this problem.

I've seen suggestions to increase the cval (https://github.com/mskcc/facets/issues/146) or lower coverage from snp-pileup i.e. use -r15,0 (https://github.com/mskcc/facets/issues/68), but I am not sure where to draw the line for these values.

Is there a place where I could find some best practice / suggested values to prevent getting purity values of NA? Any other suggestions would be a great help too

Thank you in advance!

veseshan commented 1 day ago

Purity is estimated a NA when there aren't any major segment with copy number aberration - focal amplifications are not helpful since several purity - copy number combinations can look the same. Have you looked at the plots of these samples which has NA as purity estimate? Are there meaningful copy number changes?