I think I am having an issue after lifting over from hg18 to hg38. The ultimate goal is to update the rsids from hg18 with the snp151 from UCSC (hg38) after lifting over the hg18 files. I have a chain file but did could not get the r packages to work so I used the below commands to first map the .map file to .bed format, then lift it over, then push it back into a map format:
awk '{print $1"\t"$4-1"\t"$4"\t"$2"\t.\t."}' plink.map > plink_hg18.bed liftOver plink_hg18.bed hg18ToHg38.over.chain.gz plink_hg38.bed plink_nomap awk '{print $1"\t"$4"\t0\t"$3}' plink_hg38.bed > plink_hg38.map
The issue is that the end goal is to update the rsids of the hg18 plink files. When I try: system("./plink2 --file plink_hg38 --make-just-bim --out newBim") .... I am getting back the error: Error: Empty .map file.
Would you know why this might be happening? Thanks.
