d3b-center / OpenPedCan-analysis

The analysis repository for the Open Pediatric Cancer Project

https://d3b-center.github.io/OpenPedCan-analysis/

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Updated analysis: focal cn module- remove bit putting germline sex from WGS to WXS samples #511

Open jharenza opened 8 months ago

jharenza commented 8 months ago

What analysis module should be updated and why?

Focal CN - remove bit putting germline sex from WGS to WXS samples, since we do this upstream in the histologies file preparation

What changes need to be made? Please provide enough detail for another participant to make the update.

Remove https://github.com/d3b-center/OpenPedCan-analysis/blob/029baa64af96721ce4b4819bc3174023827f4090/analyses/focal-cn-file-preparation/01-add-ploidy-cnvkit.Rmd#L31-L57

What input data should be used? Which data were used in the version being updated?

When do you expect the revised analysis will be completed?

Who will complete the updated analysis?

jharenza commented 2 months ago

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