PR 1 of n: README with first part of SNV caller analysis

[cansavvy]

Purpose/implementation

Preparing a pipeline to perform an initial analysis and calculation of each MAF file for each SNV caller. At this point, the SNV callers that will be evaluated are MuTect2, Strelka2, VarDict, and Lancet.

Issue

For SNV caller comparison #103 and Tumor Mutation Burden #3

Directions for reviewers

For this first Draft PR, I'm just pushing the README I've created for this analysis so I can get overall advice on this pipeline. If it's too difficult to evaluate this without the code, let me know and I will reformulate my PR.

Main things I am looking for advice on:

• Does the file structure and organization seem reasonable?
• Do the calculation overviews and analyses included make sense?
• Are the functions a sensible way to organize the steps for these data? (I suspect you may need to see the actual functions to really fully evaluate this question).

I will continue working on the wording of this document, so do worry about wording/grammar too much, unless my wording at any point is making it difficult to understand, then please let me know.

Results

No results just yet, because we don't yet have all the data.

Docker and continuous integration

These things will be in a future PR.

• 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.

[jaclyn-taroni]

@cansav09 I am assuming that you may have put together the table of contents here manually. We use this package for the refine.bio README ToC IIRC: https://www.npmjs.com/package/doctoc just FYI

[cansavvy]

@cansav09 I am assuming that you may have put together the table of contents here manually. We use this package for the refine.bio README ToC IIRC: https://www.npmjs.com/package/doctoc just FYI

Oh nice. Didn't know such things existed.

[jaclyn-taroni]

Couple small things. This seems like a reasonable plan to me. I feel like I can't thoroughly evaluate the functions without looking at the code. Would be good to have @jashapiro give this a once over as well.

[jaclyn-taroni]

@cansav09 can I mark this as ready for review?

[jashapiro]

Looks good to me. I expect there will be changes as the other PRs come in.

[jaclyn-taroni]

👍 We'll get this merged in and then up date it as needed.