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'
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
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'