empty microarray CNV plots on clinseq-builds.

genome / gms

The Genome Modeling System installer

https://github.com/genome/gms/wiki

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empty microarray CNV plots on clinseq-builds. #143

Closed gatoravi closed 10 years ago

gatoravi commented 10 years ago

The clinseq builds have not CNV plots. This is because the microarray files "tumor.copynumber.original" and "normal.copynumber.original" have a different format on the sGMS compared to TGI. The wrong columns are then used by the tool to call CNV's.

malachig commented 10 years ago

@gatoravi what ever happened with this issue?

gatoravi commented 10 years ago

this was fixed in master but not merged into gms-pub. I cherry-picked this change here https://github.com/genome/gms-core/commit/466aaafedd68cba0d43afda20ad9e3e75ea80b39 A new clinseq model build was run and the plots are generated correctly now. Closing this issue.