Advntr
Introduction
Advntr
is a tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data.
For more information, please check its website: https://biocontainers.pro/tools/advntr and its home page on Github.
Versions
1.4.0
1.5.0
Commands
advntr
Module
You can load the modules by:
module load biocontainers
module load advntr
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 Advntr on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=advntr
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers advntr
advntr addmodel -r chr21.fa -p CGCGGGGCGGGG -s 45196324 -e 45196360 -c chr21
advntr genotype --vntr_id 1 --alignment_file CSTB_2_5_testdata.bam --working_directory working_dir