Update manta FILTER=='PASS' Part3: oncoprint rerun

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Rerun with FILTER==PASS for manta calls used in copy_number_consensus_call

What was your approach?

Rerun

What GitHub issue does your pull request address?

AlexsLemonade#1113

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

Which areas should receive a particularly close look?

NA

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?

Results

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

What is your summary of the results?

Reproducibility Checklist

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

Documentation Checklist

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