https://github.com/kundajelab/1kg_ld_utils
utils/notes for LD calculation from 1000 genomes panel
Science Score: 10.0%
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Low similarity (4.5%) to scientific vocabulary
Last synced: 4 months ago
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Repository
utils/notes for LD calculation from 1000 genomes panel
Basic Info
- Host: GitHub
- Owner: kundajelab
- License: mit
- Language: Shell
- Default Branch: main
- Size: 47.9 KB
Statistics
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 0
Created about 5 years ago
· Last pushed about 5 years ago
https://github.com/kundajelab/1kg_ld_utils/blob/main/
## If using hg38: 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` ## If using hg19: 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.
Owner
- Name: Kundaje Lab
- Login: kundajelab
- Kind: organization
- Location: Stanford University
- Website: http://anshul.kundaje.net
- Repositories: 117
- Profile: https://github.com/kundajelab
Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.