NGS Admix

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Tyler Kent edited this page Sep 9, 2015 · 2 revisions

NGS Andmix admixture calculation. See NgsAdmix for full details on this method.

To use this method, you would run:

bash ./scripts/ADMIX.sh ./scripts/ADMIX_TAXON.conf

with the proper taxon name filled in.

Input files

Scripts

scripts/ADMIX.sh
scripts/ADMIX_TAXON.conf

Necessary input files

data/TAXON_samples.txt bam list
data/TAXON_F.txt inbreeding coefficients

Output files

results/TAXON_DerivedSFS

Mandatory `ADMIX_TAXON.conf` Variables

TAXON
K number of ancestral populations (will default to 5 if not entered)

Optional `ADMIX_TAXON.conf` Variables

N_CORES number of cores (default=32)
MIN_MAF minimum minor allele frequency filter (default=0.05)