CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between …

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.

Why CrossMap ?¶. Full genome sequencing, especially mammalian (eg. human) genomes, requires extensive, continuous efforts. Therefore reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert results that have been analyzed …