Check switch site positions in HMM copying paths

szhan / onekg_analysis

Evaluation of genotype imputation methods using the unified genealogy dataset

MIT License

0 stars 0 forks source link

Check switch site positions in HMM copying paths #18

Closed szhan closed 1 year ago

szhan commented 1 year ago

Switches should happen only at chip sites, not between chip sites. This should be a sanity check. Also, I wonder if there are hotspots of switching, even though no recombination map is provided.

szhan commented 1 year ago

I checked this from the latest runs. Switching occurs only at chip sites in those runs. Also, there seems to be some regions with a higher density of switching sites.

szhan commented 1 year ago

Continuing this in #19