Crossmap

Introduction

Crossmap is a program for genome coordinates conversion between different assemblies.

For more information, please check its website: https://biocontainers.pro/tools/crossmap and its home page: https://crossmap.readthedocs.io/en/latest/#convert-maf-format-files.

Versions

0.6.3

Commands

CrossMap.py

Module

You can load the modules by:

module load biocontainers
module load crossmap

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Crossmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=crossmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers crossmap

CrossMap.py bed GRCh37_to_GRCh38.chain.gz test.bed