Estimate initial global ancestry proportion

[mike-w-wilson]

Use ADMIXTURE to sanity check admixture proportions

• correlation between RFMix and ADMIXTURE
• Tractor paper supplementary figure 1C,E

[mike-w-wilson]

use ADMIXTURE

[mike-w-wilson]

Ran Alicia's lai_global script after creating bed files with collapse_ancestry.py as a sanity check to see how the current pipeline matches up with admixtures k=3 output. Hexplots attached for each ancestry.

Parsed lai_globals output into homogeneous, 2-way admixed, and 3-way admixed using a 5% ancestry inclusion threshold. 5% of gnomAD labeled amr individuals are homogeneous, 60% are 2-way admixed, and 35% are 3-way admixed. Of the 5% homogeneous, ~110 are homogeneous for NatAm ancestry while ~250 are EUR ancestry.