Open jaclyn-taroni opened 4 years ago
This is beyond the scope of this particular ticket but MutSigCV related things that I also found that could be helpful (with minimal commentary): I happened upon this Biostars thread and one of the answers mentioned CovGen and the CovGen docs state:
MutSig provides a "territory" table (exome_full192.coverage.txt) for times when detailed coverage information is not available for each sample in your cohort. This coverage file may not properly represent the target space utilized by your capture kit and can adversely affect the results of your MutSig analysis. CovGen bridges the gap between detailed sample level coverage information and the exome_full192.coverage.txt table that MutSig provides with a target specific full coverage table.
Splitting up #529 into more focused tickets. This is related to #517.
We are interested in trying out MutSigCV for this project. I am recording what I've found so far. Here's where we can download MutSigCV from: https://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz
MutSigCV requires MATLAB R2013a Runtime to be installed, which we can probably install with:
Note I'm extrapolating from the other things we've done so far, this is untested!
The instructions from the MutSigCV README.txt for setting up
LD_LIBRARY_PATH
are:where
mcr_root
should be/opt/mcr/v81
. We're going to have multiple versions of MCR installed, so I'm inclined to deal with the setting and unsetting ofLD_LIBRARY_PATH
in the bash scripts that run a particular tool – here's the GISTIC example:https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/56f82b9f23d369a5e208c7564ce8fc22fa0b64dd/analyses/run-gistic/scripts/run-gistic-openpbta.sh#L5
and
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/56f82b9f23d369a5e208c7564ce8fc22fa0b64dd/analyses/run-gistic/scripts/run-gistic-openpbta.sh#L68