Software: AlignStats
Description
AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.
Available Versions
| Unspecified: | 0.9.1 |
|---|
BioContainers: https://biocontainers.pro/tools/alignstats
Home page: https://github.com/jfarek/alignstats
Commands
- alignstats
Module
You can load the modules by:
module load biocontainers
module load alignstats
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run alignstats on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=alignstats
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers alignstats
alignstats -C -i input.bam -o report.txt