transvar
Link to section 'Introduction' of 'transvar' Introduction
Transvar is a multi-way annotator for genetic elements and genetic variations.
Docker hub: https://hub.docker.com/r/zhouwanding/transvar and its home page: https://bioinformatics.mdanderson.org/public-software/transvar/.
Link to section 'Versions' of 'transvar' Versions
- 2.5.9
Link to section 'Commands' of 'transvar' Commands
- transvar
Link to section 'Module' of 'transvar' Module
You can load the modules by:
module load biocontainers
module load transvar
Link to section 'Example job' of 'transvar' Example job
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 Transvar on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=transvar
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers transvar
# set up databases
transvar config --download_anno --refversion hg19
# in case you don't have a reference
transvar config --download_ref --refversion hg19
transvar panno -i 'PIK3CA:p.E545K' --ucsc --ccds