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.
module spider crossmap to find out what environment modules are available for this application.
- HPC_CROSSMAP_DIR - installation directory
If you publish research that uses crossmap you have to cite it as follows: