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harrispopgen / mutyper

Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
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Add State of the field #45

Closed izabelcavassim closed 1 year ago

izabelcavassim commented 1 year ago

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I don't see anything describing the state of the field in here: https://github.com/harrispopgen/mutyper/blob/master/paper/paper.md Can you please add that?

Maybe https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00854-6 could be one example of software comparable to mutyper.

wsdewitt commented 1 year ago

In PR #47 we've added several citations and expanded the second paragraph of the Statement of need section (the most recent pdf draft in that PR is downloadable as the artifact of this action). Although there are several methods for extracting mutation spectra for somatic mutation data, they don't scale well to population genomic germline mutation data (with thousands of individuals and millions of variants), or are not configurable/flexible (e.g. to handle diploid or haploid data). Some of these issues are discussed in the Helmsman paper (Carlson et al.).