Using other IBD segment detection tools - Githubissues

sdtemple / isweep

Statistical inference of recent positive selection using IBD segments

https://github.com/sdtemple/isweep

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Using other IBD segment detection tools #6

Closed sdtemple closed 3 months ago

sdtemple commented 3 months ago

The pipelines are built to run hap-ibd.jar and ibd-ends.jar.

sdtemple commented 3 months ago

You can use any IBD segment detection software you prefer.

The method should result in few false positives and few false negatives.

If you use another IBD detection tool, use the rules/ in workflow/ pipelines as a blueprint.

See this paper for a non-independent benchmarking of some methods.

https://doi.org/10.1093/gigascience/giac111

Some methods vetted on human data:

hap-ibd.jar + ibd-ends.jar
iLASH
Rapid
TPBWT
FastSMC + GERMLINE2

Some methods vetted on haploid Plasmodium falciparum data:

hmmIBD : https://malariajournal.biomedcentral.com/articles/10.1186/s12936-018-2349-7
isoRelate : https://doi.org/10.1371/journal.pgen.1007279
An applied data analysis : https://www.nature.com/articles/s41467-024-46659-0