Lifting over bed file with REF ALT and RSIDs
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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.

liftover • 398 views
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