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@ACEnglish ACEnglish released this 10 Dec 16:47
· 37 commits to main since this release
v1.0.1
64f7c78

Faster, Smaller, More Accurate Genotyping

Kanpig now has sub-commands gt and plup. The new plup command will extract reads and their SVs from a bam file into a small file that's useful for long-term storage of reads.

  • gt improvements:
    • can parse plup files much more quickly (up to 8x) than parsing a bam. Though bam parsing is also now ~2x faster.
    • parse PS and HP information from haplotagged reads to increase genotyping accuracy as well as record long-range phasing information in the output VCF.
    • now uses kmedoid clustering instead of kmeans, resulting in a modest improvement to genotyping accuracy.

Full Updates: https://github.com/ACEnglish/kanpig/wiki/Updates#v101
Full Changelog: v0.3.1...v1.0.1

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