Source vcf files of 1000G phase 3, hg38 downloaded from: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/
1000g hg38 phase 3 plink & vcf files are on oak:
/oak/stanford/groups/akundaje/refs/1000genomes
SNPs from "1000G.phase3.hg38.merged-merge.missnp" were multi-allelic, so removed from the 1000G Phase 3 VCF file set before creating the PLINK bed files.
- The code to generate the plink files from the souce VCF files is in
makebed/make_bed_1kg.sh - The code to filter the resulting bed/bim/fam files to Caucasian genotypes is in
getcaucasian/get_samples_to_keep.sh - The code to calculate r^2 LD values for a GWAS summary stats file is in
get_ld.sh
bed/bim/fam files are on oak in /oak/stanford/groups/akundaje/refs/1000genomes/hg19
ethnicity filtering can be done with same approach as hg38 (see getcaucasian/get_samples_to_keep.sh)
Alternatively to the workflow described for hg38,Peyton Greenside has pre-computed LD for hg19, with those files here:
/mnt/lab_data/kundaje/users/pgreens/LD
these are cited on zenodo: https://zenodo.org/record/3404275#.X9GGBpNKgxM
So you can grep for the rsid's of interest in these files.