SAMtools-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1. | 1.3.1 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Description === | === Description === | ||
" | "Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format" | ||
More details are at [http://www.htslib.org/ SAMtools] | More details are at [http://www.htslib.org/ SAMtools] | ||
=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/eb/SAMtools/1. | The last version of this application is at /usr/local/apps/eb/SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2 | ||
To use this version, please load the module with | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml SAMtools/1. | ml SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2 | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml SAMtools/1. | ml SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2<br> | ||
samtools <u>[options]</u><br> | samtools <u>[options]</u><br> | ||
</div> | </div> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml SAMtools/1. | ml SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2 | ||
samtools --help | samtools --help | ||
Program: samtools (Tools for alignments in the SAM format) | Program: samtools (Tools for alignments in the SAM format) | ||
Version: 1. | Version: 1.3.1 (using htslib 1.3.2) | ||
Usage: samtools <command> [options] | Usage: samtools <command> [options] | ||
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targetcut cut fosmid regions (for fosmid pool only) | targetcut cut fosmid regions (for fosmid pool only) | ||
addreplacerg adds or replaces RG tags | addreplacerg adds or replaces RG tags | ||
-- File operations | -- File operations |
Revision as of 14:07, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
1.3.1
Author / Distributor
Description
"Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format" More details are at SAMtools
Running Program
The last version of this application is at /usr/local/apps/eb/SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2
To use this version, please load the module with
ml SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2
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/1.3.1-foss-2016b-HTSlib-1.3.2
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/1.3.1-foss-2016b-HTSlib-1.3.2 samtools --help Program: samtools (Tools for alignments in the SAM format) Version: 1.3.1 (using htslib 1.3.2) 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 -- 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