Entering edit mode
2.2 years ago
4galaxy77
2.9k
I've got a bed file which is like this (ignore the double RSID cols):
chr17 52 52 rs556541063 rs556541063 A C 0.999393
chr17 56 56 rs145615430 rs145615430 T C 0.999695
chr17 78 78 rs148170422 rs148170422 C G 0.999939
I'd like to lift it from b37 to b38. I've been using UCSC liftOver, but this only lifts over the start/end coordinates and not also the REF / ALT alleles or RSIDs.
Is there a method which also lifts over these fields? I'd prefer a tool which inputs/outputs bed files since these are imputation data with 90m+ SNPs and I don't have the disk space to convert to e.g. vcf.