A script Assoc_P_vs_AF_Diffs.R and dataset containing sparse matrices of allele frequency differences within the
5 broad genetic ancestral groups (AFR, AMR, EAS, EUR, SAS).
** Ancestry-specific matrices yet to be provided **
R libraries required: data.table, r2r, ggplot2, optparse.
Help using this R script call be called using -h or --help
Rscript Assoc_P_vs_AF_Diffs.R -h
Usage: Assoc_P_vs_AF_Diffs.R [options]
Options:
-s STUDY, --study=STUDY
study name (no spaces) (required)
-g GWAS, --gwas=GWAS
REGENIE results filename (required)
-a ANCESTRY, --ancestry=ANCESTRY
Genetic ancestry of study: AFR|AMR|EAS|EUR|SAS (required)
-r REFDIR, --refdir=REFDIR
Main directory holding 1000G frequency data (required)
-o OUTDIR, --outdir=OUTDIR
Output directory for results. Default: ./
-h, --help
Show this help message and exit
Example command:
Rscript Assoc_P_vs_AF_Diffs.R \
--study MY_STUDY \
--gwas gwas_results.txt \
--ancestry EUR \
-r /path/to/1000g_build38_pop_freq_diffs_by_subancestry/ \
-o /path/to/output/directory/
Differences in allele frequencies across the 5 super-ancestries and 26 sub-ancestries in the 1000G Project have been calculated
for 78,122,255 autosomal variants in 2,584 indivuals.
Data is stored in a Zenodo repo here: https://zenodo.org/doi/10.5281/zenodo.11635380
The data is split by chromosome with the file extensions .pop, .var, .bin.
The file specification can be found here.
An example Python script and SNP list for lookup have been provided for use. For example, to lookup frequency differences of the subset
of 12,111 height variants published in Yengo et al on chromosome 1 across ancestral groups in the 1000G project, the following command
can be used:
python GetFreqDiffs.py \
--freq-diffs 1000g_build38_pop_freq_diffs_1 \
--vars 12111_height_snps.txt \
--out 12111_height_snps_1000g_freq_diffs_1.txt