Difference between revisions of "CrossMap"

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==System Variables==
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==

Revision as of 21:02, 6 December 2019


crossmap website  

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.

Required Modules


  • crossmap

System Variables

  • HPC_CROSSMAP_DIR - installation directory


If you publish research that uses crossmap you have to cite it as follows:

Zhao, H., Sun, Z., Wang, J., Huang, H., Kocher, J.-P., & Wang, L. (2013). CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics (Oxford, England), btt730.