custom_db

Script used to pull out SNPs present in database and 23andMe file, sort by F_ST, and write top n_snps to gzipped out_file

Package dependencies:

• pandas
• commanderline

custom_db arguments (and defaults if defined):

--db_gz

--gt_23andMe_gz

--n_snps=100000

--out_file_gz='out_custom_db.txt.gz'

validate_bootstrap

Script that takes into account bootstrap replicates and outputs estimated "super-ancestries". Main input is a text file, where the first line is the .Q output filename of a regular Ancestry run and remaining lines are the .Q files of bootstrap replicates.

Details about Ancestry: https://bitbucket.org/joepickrell/ancestry

Package dependencies:

• pandas
• commanderline

validate_bootstrap arguments (and defaults if defined):

--file_list

--negligible_threshold=0.01

--bootstrap_confidence=0.8

calc_fst

Helper script to calculate F_ST for Ancestry-format reference files. Output is the input file with an additional column named 'fst' (SNPs with NaN for F_ST are removed)

Details about Ancestry: https://bitbucket.org/joepickrell/ancestry

Package dependencies:

• pandas
• commanderline

calc_fst arguments (and defaults if defined):

--ref_gz

--out_gz='out_db_fst.txt.gz'