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getzlab / deTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
BSD 3-Clause "New" or "Revised" License
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Results #18

Closed MagdalenaZZ closed 6 years ago

MagdalenaZZ commented 6 years ago

screen shot 2018-10-18 at 10 14 38

Hi, I've run deTIN on a truth-set of artificially created TIN from 1-30%, for two samples. The results file is attached. Two thoughts;

  1. I seem to get higher score with aSCGC than with SSNV.
  2. aSCG at very low levels of containation seem to report artificially high values.

Have you got any advice to offer to improve/interpret the results?

Also, I've noticed that even with 1% TIN contamination my SNV calling looses a lot of accuracy, do you believe deTIN can be tuned to discover such low levels of TIN?

Many thanks for your input!

MagdalenaZZ commented 6 years ago

I set the tin-prior to 0.01 for all samples, to try to pull them towards the lower solution

amarotaylor commented 6 years ago

Hey Magalena,

Looks good overall though I agree that 1 and 2 look could be issues. I think it might be easier for me to offer advice via a google hangout or longer emails. Can you drop me an email at amaro@broadinstitute.org so we can discuss?