Investigate Tractor script for counting bug

broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference

MIT License

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Investigate Tractor script for counting bug #108

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

Tractor output is reporting fewer ancestry counts than expected for the SLC variant. There is likely a bug somewhere within the script that is miscounting ancestry haplotypes or alternate alleles.

mike-w-wilson commented 3 years ago

If a VCF site started before the MSP window, tractor read the entire MSP file and then used the last window for all sites in the VCF. This was fixed in a Tractor PR https://github.com/eatkinson/Tractor/pull/10