Consensus seg update for oncoplot

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

We are adding CNV calls from consensus seg files for autosomes , X and Y chromosomes as inputs for oncoplots.

What was your approach?

Update the input files to :

consensus_seg_autosomes_cnv_file=${focal_directory}/consensus_seg_annotated_cn_autosomes.tsv.gz
consensus_seg_cnv_xy_cnv_file=${focal_directory}/consensus_seg_annotated_cn_x_and_y.tsv.gz

What GitHub issue does your pull request address?

1087

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

The figures need careful review , the only update in consensus seg files and we are currently coding loss as "Del" and amplification and gain as "Amp" to match the maftools requirements as in #1009

Is there anything that you want to discuss further?

Na

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

figures

What is your summary of the results?

ATRX calls are now added with use of X and Y chromosome calls and all CNV overlapping gene locations are being plotted.

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[jaclyn-taroni]

Just re-requested @jharenza, I'm going to wait to review #1092 until this gets another look

[jharenza]

Thanks, I took a brief look yesterday, but think we also need a "deep deletion filter", as hemizygous deletions aren't usually shown in the oncoprints, but I need to think and read about this a little more before proposing a threshold.

[jaclyn-taroni]

Thanks, I took a brief look yesterday, but think we also need a "deep deletion filter", as hemizygous deletions aren't usually shown in the oncoprints, but I need to think and read about this a little more before proposing a threshold.

Is that filter necessary for this PR or can it be done later, in a separate pull request, once you have had a chance to read and digest some material?

[jharenza]

Thanks, I took a brief look yesterday, but think we also need a "deep deletion filter", as hemizygous deletions aren't usually shown in the oncoprints, but I need to think and read about this a little more before proposing a threshold.

Is that filter necessary for this PR or can it be done later, in a separate pull request, once you have had a chance to read and digest some material?

We can do later, thanks!