I obtained a bunch of snp Array data from the 23andme website. The raw data output looks like this. I want to convert it from human reference build 36 to human reference build 37. I know one solution is to convert it with Liftover.
Liftover requires the format to be in bed format. I converted the file raw data into bed format but notice that the raw data output from 23andme does not have a chromosome start and chromosome end. So what I did was use the position as the chromosome start and chromosome end.
Once I obtained the bed file, I tried running the Liftover command to convert from build 36 to build 37
./liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed
It runs fine but nothing appears in the output.bed file. The chain file is not picking up the snp location so it's not working properly.
Does anyone know how I can convert the output from 23andme into build 37? thanks