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harrispopgen / mutyper

Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
7 stars 3 forks source link

polarize genotypes, closes #17 #18

Closed wsdewitt closed 3 years ago

wsdewitt commented 3 years ago

Patch to fix #17. Now genotypes are polarized the ancestral state

wsdewitt commented 3 years ago

This appears to be fixed, e.g. the errant line in issue is now.

NW_020656121.1  91648257    .   A   C   .   PASS    AA=T;AC=1;AN=68;mutation_type=AAT>ACT;AF=0.0147059  GT  0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0