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harrispopgen / mushi

[mu]tation [s]pectrum [h]istory [i]nference
https://harrispopgen.github.io/mushi/
MIT License
24 stars 6 forks source link

1kg #26

Closed wsdewitt closed 5 years ago

wsdewitt commented 5 years ago

This branch adds support for processing 1000 Genomes SNP data, and also includes various revisions to the underlying mushi library.

Notebook 1KG.ipynb shows results on a 1KG 3-SFS.

Review is needed from @kharris on the accelerated proximal gradient descent code: https://github.com/harrispopgen/mushi/blob/90dccc3c34f726c7c75d7311c783941b1849ba19/mushi.py#L341-L527

Perhaps @WSDeWitt and @kelleyharris can chat through the 1KG pipeline: https://github.com/harrispopgen/mushi/blob/90dccc3c34f726c7c75d7311c783941b1849ba19/1KG/SConstruct#L1-L136