SAMtools-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1. | 0.1.20, 1.6, 1.14, 1.16.1, 1.17 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Description === | === Description === | ||
"SAM Tools provide various utilities for manipulating alignments in the SAM 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 === | ||
'''Version 0.1.20''' | |||
Installed in /apps/eb/SAMtools/0.1.20-GCC-11.2.0 | |||
To use this version, please load the module with | |||
<pre class="gscript"> | |||
ml SAMtools/0.1.20-GCC-11.2.0 | |||
</pre> | |||
'''Version 1.6''' | |||
Installed in /apps/eb/SAMtools/1.6-GCC-11.2.0 | |||
To use this version, please load the module with | |||
<pre class="gscript"> | |||
ml SAMtools/1.6-GCC-11.2.0 | |||
</pre> | |||
'''Version 1.14''' | |||
Installed in /apps/eb/SAMtools/1.14-GCC-11.2.0 | |||
To use this version, please load the module with | |||
<pre class="gscript"> | |||
ml SAMtools/1.14-GCC-11.2.0 | |||
</pre> | |||
'''Version 1.16.1''' | |||
Installed in /apps/eb/SAMtools/1.16.1-GCC-11.3.0 | |||
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. | ml SAMtools/1.16.1-GCC-11.3.0 | ||
</pre> | </pre> | ||
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=SAMtools.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=SAMtools.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=SAMtools.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml SAMtools/1. | ml SAMtools/1.16.1-GCC-11.3.0<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/1.16.1-GCC-1.3.0 | ||
samtools --help | |||
Program: samtools (Tools for alignments in the SAM format) | Program: samtools (Tools for alignments in the SAM format) | ||
Version: 1. | Version: 1.16.1 (using htslib 1.16) | ||
Usage: samtools <command> [options] | Usage: samtools <command> [options] | ||
Line 70: | Line 101: | ||
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 76: | Line 108: | ||
fixmate fix mate information | fixmate fix mate information | ||
reheader replace BAM header | reheader replace BAM header | ||
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 | ||
markdup mark duplicates | |||
ampliconclip clip oligos from the end of reads | |||
-- File operations | -- File operations | ||
collate shuffle and group alignments by name | collate shuffle and group alignments by name | ||
cat concatenate BAMs | cat concatenate BAMs | ||
consensus produce a consensus Pileup/FASTA/FASTQ | |||
merge merge sorted alignments | merge merge sorted alignments | ||
mpileup multi-way pileup | mpileup multi-way pileup | ||
Line 90: | Line 124: | ||
fastq converts a BAM to a FASTQ | fastq converts a BAM to a FASTQ | ||
fasta converts a BAM to a FASTA | fasta converts a BAM to a FASTA | ||
import Converts FASTA or FASTQ files to SAM/BAM/CRAM | |||
reference Generates a reference from aligned data | |||
-- 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 | ||
Line 98: | Line 135: | ||
phase phase heterozygotes | phase phase heterozygotes | ||
stats generate stats (former bamcheck) | stats generate stats (former bamcheck) | ||
ampliconstats generate amplicon specific stats | |||
-- Viewing | -- Viewing | ||
flags explain BAM flags | flags explain BAM flags | ||
head header viewer | |||
tview text alignment viewer | tview text alignment viewer | ||
view SAM<->BAM<->CRAM conversion | view SAM<->BAM<->CRAM conversion | ||
depad convert padded BAM to unpadded BAM | depad convert padded BAM to unpadded BAM | ||
samples list the samples in a set of SAM/BAM/CRAM files | |||
-- Misc | |||
help [cmd] display this help message or help for [cmd] | |||
version detailed version information | |||
</pre> | </pre> |
Latest revision as of 09:33, 14 May 2024
Category
Bioinformatics
Program On
Teaching
Version
0.1.20, 1.6, 1.14, 1.16.1, 1.17
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 0.1.20
Installed in /apps/eb/SAMtools/0.1.20-GCC-11.2.0
To use this version, please load the module with
ml SAMtools/0.1.20-GCC-11.2.0
Version 1.6
Installed in /apps/eb/SAMtools/1.6-GCC-11.2.0
To use this version, please load the module with
ml SAMtools/1.6-GCC-11.2.0
Version 1.14
Installed in /apps/eb/SAMtools/1.14-GCC-11.2.0
To use this version, please load the module with
ml SAMtools/1.14-GCC-11.2.0
Version 1.16.1
Installed in /apps/eb/SAMtools/1.16.1-GCC-11.3.0
To use this version, please load the module with
ml SAMtools/1.16.1-GCC-11.3.0
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/1.16.1-GCC-11.3.0
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/1.16.1-GCC-1.3.0 samtools --help Program: samtools (Tools for alignments in the SAM format) Version: 1.16.1 (using htslib 1.16) 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 ampliconclip clip oligos from the end of reads -- File operations collate shuffle and group alignments by name cat concatenate BAMs consensus produce a consensus Pileup/FASTA/FASTQ 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 import Converts FASTA or FASTQ files to SAM/BAM/CRAM reference Generates a reference from aligned data -- 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) ampliconstats generate amplicon specific stats -- Viewing flags explain BAM flags head header viewer tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM samples list the samples in a set of SAM/BAM/CRAM files -- Misc help [cmd] display this help message or help for [cmd] version detailed version information
Installation
Source code is obtained from SAMtools
System
64-bit Linux