Updated analysis: copy_number_consensus_call and focal-cn-file-preparation for OT

[kgaonkar6]

What analysis module should be updated and why?

focal-cn-file-preparation, to include the neutral calls in output files and add gene annotated cnvkit seg files for WXS samples.

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

• Keep neutral calls here
  https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/0b5099f94038e12a7e1d98cc65b0801bca8ded63/analyses/focal-cn-file-preparation/04-prepare-cn-file.R#L237-L238
  and
  https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/0b5099f94038e12a7e1d98cc65b0801bca8ded63/analyses/focal-cn-file-preparation/04-prepare-cn-file.R#L262-L263

• Add annotated cnvkit seg files with:
  https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/0b5099f94038e12a7e1d98cc65b0801bca8ded63/analyses/focal-cn-file-preparation/run-prepare-cn.sh#L80

• Also carry over changes needed for deep deletion from Updated deep loss CNV calls  AlexsLemonade/OpenPBTA-analysis#1101

• As delivery for pedcbio we will add another script that combines
  - consensus_seg_annotated_cn_autosomes.tsv.gz
  - consensus_seg_annotated_cn_x_and_y.tsv.gz
  - cnvkit_annotated_cn_autosomes.tsv.gz filtered for WXS samples only
  - cnvkit_annotated_cn_x_and_y.tsv.gz filtered for WXS sample only

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

cnv-cnvkit.seg.gz
cnv-controlfreec.tsv.gz

When do you expect the revised analysis will be completed?

1 day

Who will complete the updated analysis?

@kgaonkar6

[kgaonkar6]

Closing this since the updated code and files are in v6