SAMtools-Teaching
Category
Bioinformatics
Program On
Teaching
Version
0.1.19, 1.3.1, 1.6
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
Version 0.1.19
Installed in /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
Version 1.3.1
Installed in /usr/local/apps/eb/SAMtools/1.3.1-foss-2016b
To use this version, please load the module with
ml SAMtools/1.3.1-foss-2016b
Version 1.6
Installed in /usr/local/apps/eb/SAMtools/1.6-foss-2016b
To use this version, please load the module with
ml SAMtools/1.6-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/1.6-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/1.6-foss-2016b samtools --help Program: samtools (Tools for alignments in the SAM format) Version: 1.6 (using htslib 1.6) Usage: samtools <command> [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header rmdup remove PCR duplicates targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA -- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) -- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM
Installation
Source code is obtained from SAMtools
System
64-bit Linux