LAmisc

Local ancestry miscellaneous

pgenlib is needed. Download here

Converting .fb.tsv to plink format

# Output test.pgen test.psam test.pvar
## Convert RFMIX2 .fb.tsv to plink format
python rfmix2pgen.py --file test.fb.tsv --out test --pop AFR

# Run genome-wide scan on example phenos
plink2 --pfile example --pheno example.pheno --glm allow-no-covars --out example