Difference between revisions of "CrossMap"
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| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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Revision as of 21:02, 6 December 2019
Description
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
Serial
- crossmap
System Variables
- HPC_CROSSMAP_DIR - installation directory
Citation
If you publish research that uses crossmap you have to cite it as follows: