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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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Creat PoN for CH #170

Open evanbiederstedt opened 5 years ago

evanbiederstedt commented 5 years ago

Refers to https://github.com/mskcc/vaporware/issues/101

--- The best approach would be to call blood normal vs. a curated pooled normal of young patients without any hematological malignancies. We do not yet have a curated "normal" though. In order to create this, "use data from the youngest patients that you have, but check that they didnt have an active heme malignancy at time of sequencing and could even genotype for the most common blood mutations to exclude samples with obvious somatic mutations in blood".

We might have this already? Not sure

evanbiederstedt commented 5 years ago

I believe @ahmetz is on the case

kpjonsson commented 5 years ago

I don't see why we wouldn't use the same panel of normals for somatic SNVs/indels for filtering CH calls as well.

evanbiederstedt commented 5 years ago

@kpjonsson We certainly could. It depends how you would want to write the methods section for any CH work.

Theoretically, you would want a PoN of young patients with no hematological abnormalities.

kpjonsson commented 5 years ago

Precisely my point. Some CH-associated mutations are somatic hotspot residues.

evanbiederstedt commented 5 years ago

It's just a matter of finding such normals...

evanbiederstedt commented 5 years ago

@hellybelly330 is going to do this, hooray

hellybelly330 commented 5 years ago

plan is to flag signed out CH variants from the normal variant calls and remove these normals

evanbiederstedt commented 5 years ago

As mentioned over a brief conversation, part of the motivation here is that we need a PoN for variant calling.

The idea was to possibly kill two birds with one stone, as it doesn't make sense to redo this work for CH.

There was also some discussion about making this assay/tissue specific. It's possible to implement that in a pipeline, but let's not get too deep in the weeds.

Let's do what we can with the samples we currently have for a standard PoN for variant calling, WES recaptures. Feel free to agree/disagree/etc. @hellybelly330 @rptashkin

More relevant: https://github.com/mskcc/vaporware/issues/126

evanbiederstedt commented 5 years ago

We'll need more samples for this