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CrossMap

http://crossmap.sourceforge.net/
  • CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).
  • It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.
  • CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.
  • We do not recommend using CrossMap to convert genome coordinates between species.