SAMtools-Teaching
Category
Bioinformatics
Program On
Teaching
Version
0.1.19
Author / Distributor
Description
"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." More details are at SAMtools
Running Program
The last version of this application is at /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b
To use this version, please load the module with
ml SAMtools/0.1.19-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_SAMtools
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SAMtools.%j.out
#SBATCH --error=SAMtools.%j.err
cd $SLURM_SUBMIT_DIR
ml SAMtools/0.1.19-foss-2016b
samtools [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml SAMtools/0.1.19-foss-2016b samtools --help [main] unrecognized command '--help'
Installation
Source code is obtained from SAMtools
System
64-bit Linux