Updated analysis: Experimental_strategy specific copy_consensus run

[kgaonkar6]

What analysis module should be updated and why?

copy_number_consensus_call currently uses all samples in the following CNV files which

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

But WGS and WXS samples need to be handled differently so the code will need update.

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

The options I see are:

1. Logic inside the code to only use WGS samples in script that creates the Snakemake file and run the module to generate 2/3 cnv caller consensus calls. (I believe this is faster because it doesn't have to separate the input merged files to the WXS files in scratch)

2. Logic to handle WGS and WXS separately with different Snakemake files as implemented by bix-ops that uses cnvkit_freec consensus calls however for OT it was decided to only use cnvkit calls for WXS ( This will help get the bixops and OT development on the same page though)

@jharenza @logstar @zhangb1 for input.

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

v7

cnv-cnvkit.seg.gz
cnv-controlfreec.tsv.gz
sv-manta.tsv.gz
histologies.tsv

When do you expect the revised analysis will be completed?

2 days

Who will complete the updated analysis?

@kgaonkar6

[jharenza]

Cc @yuankunzhu as well

[jharenza]

Note: filenames will also need to be updated

[jharenza]

@runjin326 can you work on part 1 as priority? then, I think @zhangb1 can use this code (part 2) in the toolkit.

[runjin326]

@jharenza, sure! I will prioritize this and I'll ping you and @zhangb1 when completed!

[runjin326]

@jharenza, hmm I am getting a bit confused right now. I think the code in this script already subset for WGS and only run for those? And I think the run script already called the right file (although the README.md does need an update)?
I also ran the code that generate the snakeMake and individual file , they all have 1276 samples which is as expected for all WGS + Tumor. Am I missing something here?

[jharenza]

Ahh, ok- I thought @kgaonkar6 did this for v7, but then saw the ticket - so maybe part 1 is complete.

[kgaonkar6]

The code is run on v7 but since we didn't add any more WGS in v8 the files in the dev branch is up-to-date.

[runjin326]

Close with PR89