plinkLiftOver

Quick liftOver for PLINK data

1. Software

• Conda
  • plink2
  • liftOver

2. Code

#Prepare conda environment

conda create --name liftOver; conda activate liftOver; conda install -c bioconda plink2; conda install -c bioconda ucsc-liftover

#download liftOver chain file

wget https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz

#liftOver hg19 to hg38

pl=YouPlinkName

#normalise IDs
awk '{$2=$1":"$4":"$6":"$5; print $0}' $pl.bim > temp; mv temp $pl.bim
#filter out duplicates, SNP with frequency <0.01, non-SNP and non-acgt variants, tri-allelic SNP
plink2 --bfile $pl --rm-dup force-first --maf 0.01 --snps-only just-acgt --output-chr M --set-hh-missing --max-alleles 2 --make-bed --out $pl.filtered
#create BED file
awk 'OFS="\t"{print "chr"$1, $4-1, $4, $2}' $pl.filtered.bim > $pl.filtered.hg19.bed
#liftOver hg19 to hg38
liftOver $pl.filtered.hg19.bed hg19ToHg38.over.chain $pl.filtered.hg38.bed unMapped
#update original PLINK file with hg38 genome positions
plink2 --bfile $pl.filtered --extract <(cut -f4  $pl.filtered.hg38.bed) --update-map <(awk '{print $4,$3}' $pl.filtered.hg38.bed) --make-bed --out $pl.filtered.hg38