Difference between exon positions in hg19 and b37?

Question

[mct2159]

I have a bunch of .bam files along with a .bed file containing the intervals for the exons. However, the .bam files are according to the b37 reference while the .bed file is according to the hg19 reference. If necessary, how can I convert the coordinates in the .bed file to a b37 reference?

Answer 1

[Pierre Lindenbaum]

Use sed to convert the names. Devon wrote a github repo containing the names in each version: https://github.com/dpryan79/ChromosomeMappings/blob/master/GRCh37_UCSC2ensembl.txt

[bjwiley23]

just for anybody who lands here first. This is updated answer using bcftools. still need Devon's file(s).