SAMtools-Teaching: Difference between revisions

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=== Version ===
=== Version ===
0.1.19, 1.3.1, 1.6
0.1.20, 1.9, 1.10
   
   
=== Author / Distributor ===
=== Author / Distributor ===
Line 21: Line 21:
=== Running Program ===
=== Running Program ===


'''Version 0.1.19'''
'''Version 0.1.20'''


Installed in /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b
Installed in /apps/eb/SAMtools/0.1.20-GCC-8.3.0


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/0.1.19-foss-2016b
ml SAMtools/0.1.20-GCC-8.3.0
</pre>  
</pre>  


'''Version 1.3.1'''
'''Version 1.9'''


Installed in /usr/local/apps/eb/SAMtools/1.3.1-foss-2016b
Installed in /apps/eb/SAMtools/1.9-GCC-8.3.0


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/1.3.1-foss-2016b
ml SAMtools/1.9-GCC-8.3.0
</pre>  
</pre>  


'''Version 1.6'''
'''Version 1.10'''


Installed in /usr/local/apps/eb/SAMtools/1.6-foss-2016b
Installed in /apps/eb/SAMtools/1.10-GCC-8.3.0


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/1.6-foss-2016b
ml SAMtools/1.10-GCC-8.3.0
</pre>  
</pre>  


Line 63: Line 63:
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml SAMtools/1.6-foss-2016b<br>     
ml SAMtools/1.10-GCC-8.3.0<br>     
samtools <u>[options]</u><br>   
samtools <u>[options]</u><br>   
</div>
</div>
Line 79: Line 79:
   
   
<pre  class="gcommand">
<pre  class="gcommand">
ml SAMtools/1.6-foss-2016b
ml SAMtools/1.10-GCC-8.3.0


samtools --help
samtools --help


Program: samtools (Tools for alignments in the SAM format)
Program: samtools (Tools for alignments in the SAM format)
Version: 1.6 (using htslib 1.6)
Version: 1.10 (using htslib 1.10)


Usage:  samtools <command> [options]
Usage:  samtools <command> [options]
Line 92: Line 92:
     dict          create a sequence dictionary file
     dict          create a sequence dictionary file
     faidx          index/extract FASTA
     faidx          index/extract FASTA
    fqidx          index/extract FASTQ
     index          index alignment
     index          index alignment


Line 98: Line 99:
     fixmate        fix mate information
     fixmate        fix mate information
     reheader      replace BAM header
     reheader      replace BAM header
    rmdup          remove PCR duplicates
     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
Line 116: Line 116:
   -- Statistics
   -- Statistics
     bedcov        read depth per BED region
     bedcov        read depth per BED region
    coverage      alignment depth and percent coverage
     depth          compute the depth
     depth          compute the depth
     flagstat      simple stats
     flagstat      simple stats

Revision as of 21:49, 27 August 2020

Category

Bioinformatics

Program On

Teaching

Version

0.1.20, 1.9, 1.10

Author / Distributor

SAMtools

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 0.1.20

Installed in /apps/eb/SAMtools/0.1.20-GCC-8.3.0

To use this version, please load the module with

ml SAMtools/0.1.20-GCC-8.3.0

Version 1.9

Installed in /apps/eb/SAMtools/1.9-GCC-8.3.0

To use this version, please load the module with

ml SAMtools/1.9-GCC-8.3.0

Version 1.10

Installed in /apps/eb/SAMtools/1.10-GCC-8.3.0

To use this version, please load the module with

ml SAMtools/1.10-GCC-8.3.0

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/1.10-GCC-8.3.0
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/1.10-GCC-8.3.0

samtools --help

Program: samtools (Tools for alignments in the SAM format)
Version: 1.10 (using htslib 1.10)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     fqidx          index/extract FASTQ
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     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
     coverage       alignment depth and percent coverage
     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


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Installation

Source code is obtained from SAMtools

System

64-bit Linux