ICGC-TCGA-PanCancer/pancancer-sandbox — pull request #4 by junjun-zhang (2014-11-30 22:52:03+00:00)
Title: added two new fields for seq coverage

Hey Keiran,

I created a shell script that calls you qc prioritization perl script: https://github.com/ICGC-TCGA-PanCancer/pancancer-sandbox/blob/develop/pcawg_metadata_parser/run_me.sh

It was not quite clear to me how the Normalised X is calculated, and the value does not seem make much sense to me. I made a patch which added two new fields in the output corresponding to normal coverage and average tumor coverage respectively. I also modified how normalised x is calculated based on my understanding.

This was done quickly and was not meant to be a proper fix, just wanted you to have a look and see whether it makes sense to you.

Thanks,
Junjun