hrc_alignment.sh

# generate frequency file
plink --bfile data/data_chr1 --freq --out results/data_chr1 --noweb

# run checking tool
HRC='/mnt/iusers01/jw01/mdeasjdb/projects/shared_resources/HRC/HRC.r1.GRCh37.autosomes.mac5.sites.tab'
perl script/HRC-1000G-check-bim.pl -b data/data_chr1.bim -f results/data_chr1.frq -r $HRC -h

# update data
sh Run-plink.sh

# convert to vcf - using --keep-allele-order
plink2 --bfile data_checked/data_chr1-updated-chr1 --a2-allele data_checked/data_chr1-updated-chr1.bim 5 2 --keep-allele-order --recode vcf --out vcf/data_chr1-updated-chr1-test3
vcf-sort vcf/data_chr1-updated-chr1-test3.vcf | bgzip > vcf/data_chr1-updated-chr1-test3.vcf.gz

# checkVCF
./check-vcf/checkVCF.py -r check-vcf/hs37d5.fa -o vcf-check/test3 vcf/data_chr1-updated-chr1-test3.vcf.gz