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Imputation Scripts

This script creates a chr23 GWAS VCF file from PLINK binary files. Overall goal is to impute it with Michigan Imputation Server. Please install Plink2 before you start.

Get all required data and tools

 wget http://www.well.ox.ac.uk/~wrayner/tools/HRC-1000G-check-bim-v4.2.9.zip
 unzip HRC-1000G-check-bim-v4.2.9.zip
 wget ftp://ngs.sanger.ac.uk/production/hrc/HRC.r1-1/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz
 gunzip HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz
 wget ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz
 wget https://github.com/seppinho/scripts/blob/master/imputation/bin/vcfCooker

Pipeline

Extract chr23 from overall binary file set (bed, bim, fam)

Info: Always specify GWAS-File without ending bed/bim/fam when using PLINK.

 plink --bfile <GWAS-file> --chr 23 --out <GWAS-file-out> --make-bed

Optional filter step

 plink --bfile <input-out> --maf 0.01 --hwe 1E-5 --geno 0.04  --out  <input-out-filtered> --make-bed

Run Wrayner Tool

 plink --freq --bfile <input-out-filtered>  --out <frequency-file> 
 perl HRC-1000G-check-bim.pl -b <input-out-filtered.bim> -f <frequency-file> -r HRC.r1-1.GRCh37.wgs.mac5.sites.tab -h
 sh Run-plink.sh
 ./vcfCooker --in-bile <updated-file> --ref human_g1k_v37.fasta --out chr23 --write-vcf
 bgzip chr23.vcf

Result

The result can be uploaded to https://imputationserver.sph.umich.edu