JOSS paper

[wsdewitt]

Hi @mrvollger @Lukez-pi @goldmich @RenzoTale88 @ab08028 @kelleyharris,

This PR adds a draft JOSS paper; you are all listed as co-authors based on your contributions to the mutyper package.

A few things about how submissions work:

• The paper content is in the markdown file here.
• A PDF is rendered automatically by a GitHub action whenever the markdown file is modified. To view the pdf, click through the most recent run and download the pdf file in the "artifacts" section.
• The review process occurs via issues on this repo submitted by editor and reviewers.

To do

1. Let me know (or discuss in this PR) any questions/comments/concerns.
2. Take a look at your affiliation and ORCID and confirm they are correct.
3. Do you have any funding acknowledgments?

Feel free to push minor edits to the markdown file, or just ask me to make changes.

[mrvollger]

Thanks for including me! My information is correct and I didn't find any typos or issues with the manuscript (though I am notoriously bad at finding these things). Feel free to change my author position to whatever re our slack discussion.

[ab08028]

This is super cool, Will! Thanks for putting this together and including me. I think it all reads well. A couple small notes:

1. It might be worth more explicitly stating what the output formats are for mutyper variants and mutyper spectrum. In particular, I think it's perhaps worth noting that mutyper variants outputs in vcf format, but the ref and alt alleles are now reverse-complemented ancestral and derived alleles, and that the 0/1 designations of the genotypes have been updated accordingly.

2. When you talk about using the chimp liftover as a means of polarization, it's not clear if that is something the user can supply directly to mutyper, or if it's just a suggestion of a method they can use to generate their ancestral fasta.

Funding-wise, my acknowledgement is: A.C.B. was supported by the Biological Mechanisms of Healthy Aging Training Program, NIH T32AG066574.

I also typically add my middle initial to my name (Annabel C. Beichman)

Let me know if I can help with anything else!