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