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broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference
MIT License
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Investigate collapse_ancestry1.py #93

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

The paint_karyograms.py script is grabbing the incorrect values in the bed files. This needs to be investigated. Bed files are skipping sections of the chromosome and may be leading to mispainting.

mike-w-wilson commented 3 years ago

This bug is rescued by a bug in the karyogram painting script but still impacts the global lai script

mike-w-wilson commented 3 years ago

A bug was found in both collapse_ancestry1.py and plot_karyogram1.py. The plot_karyogram1.py bug rescues the collapse ancestry. Collapse_ancestry1.py has a fence post problem where the last window in a file is not being added for the ancestry in the bed file. This creates gaps on the right side of the ancestry windows in the karyograms. Plot ancestry rescues this by grabbing the incorrect field, bp, and plotting the rectangles from a cM position to the bp position instead of cM to cM. This fills in the gap as the anc rectangle extend off the plotted areas.

This has not been fixed as it is not urgent. Closing and opening an issue to fix plotting in icebox.