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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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CCS question: what about germline CNVs? #380

Open evanbiederstedt opened 5 years ago

evanbiederstedt commented 5 years ago

Put on roadmap, talk to @md09

""" Someone verify for me this captures germline CNVs? If not, we need to put that on a future roadmap. """

kpjonsson commented 5 years ago

Within the abilities of what Manta and Delly.

Delly: "For an insert size of 200-300bp with a 20-30bp standard deviation, Delly starts to call reliable SVs >=300bp."

Manta: can call insertions and deletions <500 bp according to their publication.

We have not implemented any method that mirrors the clinical pipeline's coverage-based method, but perhaps might not need it if the Manta/Delly combo is sensitive enough.

evanbiederstedt commented 5 years ago

We have not implemented any method that mirrors the clinical pipeline's coverage-based method, but perhaps might not need it if the Manta/Delly combo is sensitive enough.

The tricky thing is that coverage-based CNV methods usually give somewhat different responses than SV calling. However....for the germline CNVs we would be interested in, just using the germline SV calls above may be a good start.

Good point