SAMtools-Teaching: Difference between revisions

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=== Version ===
=== Version ===
0.1.19
1.6
   
   
=== Author / Distributor ===
=== Author / Distributor ===
Line 16: Line 16:
   
   
=== Description ===
=== 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."
"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 [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/0.1.19-foss-2016b
The last version of this application is at /usr/local/apps/eb/SAMtools/1.6-foss-2016b


To use this version, please loads 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/1.6-foss-2016b  
</pre>  
</pre>  


Here is an example of a shell script, sub.sh, to run on at the batch queue:  
Here is an example of a shell script, sub.sh, to run on the batch queue:  


<div class="gscript2">
<div class="gscript2">
Line 42: Line 42:
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml SAMtools/0.1.19-foss-2016b<br>     
ml SAMtools/1.6-foss-2016b<br>     
samtools <u>[options]</u><br>   
samtools <u>[options]</u><br>   
</div>
</div>
Line 58: Line 58:
   
   
<pre  class="gcommand">
<pre  class="gcommand">
ml SAMtools/0.1.19-foss-2016b  
ml SAMtools/1.6-foss-2016b  
samtools samtools --help
samtools samtools --help
[main] unrecognized command '--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
 


</pre>
</pre>

Revision as of 13:47, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

1.6

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

The last version of this application is at /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

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 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


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Installation

Source code is obtained from SAMtools

System

64-bit Linux