Add support for FusionCatcher

Open iskandr opened this issue 9 years ago • 4 comments

Identifies fusion proteins from RNAseq and also catches expression of viral sequences:

https://github.com/ndaniel/fusioncatcher

Sep 29 '16 23:09 iskandr

May also want to consider https://sites.google.com/site/bioericscript as it's what UCSC's ProTECT uses for fusion calling in their neoepitope selection pipeline.

Sep 29 '16 23:09 hammer

I actually did this at some point: https://github.com/hammerlab/biokepi/commit/4f3449d4f7bd06bde609b7a759daf6d59e883ad6

I'm 80% certain this worked, but will re-test and submit a PR. The issue was that on many, many BAMs this required > 60 GB memory and would fail, which was really unfortunate.

Sep 30 '16 00:09 arahuja

Grab a highmem type! https://cloud.google.com/compute/docs/machine-types

Sep 30 '16 00:09 hammer

Yea that is actually what spurred my move to gcloud originally, got a 128G machine to run all of our samples through.

Sep 30 '16 00:09 arahuja