SAMtools-Teaching - Revision history

Shtsai at 01:32, 5 April 2026

2026-04-05T01:32:41Z

← Older revision		Revision as of 21:32, 4 April 2026
Line 1:		Line 1:
	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==
	0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21		0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21

	=== Author / Distributor ===		== Author / Distributor ==

	[http://www.htslib.org/ SAMtools]		[http://www.htslib.org/ SAMtools]

	=== 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 ==

	'''Version 0.1.20'''		'''Version 0.1.20'''
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from [http://www.htslib.org/ SAMtools]		Source code is obtained from [http://www.htslib.org/ SAMtools]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 20:48, 9 January 2026

2026-01-09T20:48:19Z

← Older revision		Revision as of 16:48, 9 January 2026
Line 23:		Line 23:
	'''Version 0.1.20'''		'''Version 0.1.20'''

	Installed in /apps/eb/SAMtools/0.1.20-GCC-11.2.0		Installed in /apps/eb/SAMtools/0.1.20-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/0.1.20-GCC-11.2.0		ml SAMtools/0.1.20-GCC-11.3.0
	</pre>		</pre>

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	ml SAMtools/1.16.1-GCC-11.3.0		ml SAMtools/1.16.1-GCC-11.3.0
	</pre>		</pre>

			'''Version 1.18'''

			Installed in /apps/eb/SAMtools/1.18-GCC-12.3.0

			To use this version, please load the module with
			<pre class="gscript">
			ml SAMtools/1.18-GCC-12.3.0
			</pre>

			'''Version 1.21'''

			Installed in /apps/eb/SAMtools/1.21-GCC-13.3.0

			To use this version, please load the module with
			<pre class="gscript">
			ml SAMtools/1.21-GCC-13.3.0
			</pre>


	Here is an example of a shell script, sub.sh, to run on the batch queue:		Here is an example of a shell script, sub.sh, to run on the batch queue:
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SAMtools/1.~~16.1~~-GCC-11.3.0<br>		ml SAMtools/1.21-GCC-13.3.0<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.~~16.1~~-GCC-1.3.0		ml SAMtools/1.21-GCC-13.3.0

	samtools --help		samtools --help

	Program: samtools (Tools for alignments in the SAM format)		Program: samtools (Tools for alignments in the SAM format)
	Version: 1.~~16.1~~ (using htslib 1.16)		Version: 1.21 (using htslib 1.21)

	Usage: samtools <command> [options]		Usage: samtools <command> [options]
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	import Converts FASTA or FASTQ files to SAM/BAM/CRAM		import Converts FASTA or FASTQ files to SAM/BAM/CRAM
	reference Generates a reference from aligned data		reference Generates a reference from aligned data
			reset Reverts aligner changes in reads

	-- Statistics		-- Statistics
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	flagstat simple stats		flagstat simple stats
	idxstats BAM index stats		idxstats BAM index stats
			cram-size list CRAM Content-ID and Data-Series sizes
	phase phase heterozygotes		phase phase heterozygotes
	stats generate stats (former bamcheck)		stats generate stats (former bamcheck)

Shtsai: /* Version */

2026-01-09T20:45:14Z

Version

← Older revision		Revision as of 16:45, 9 January 2026
Line 9:		Line 9:

	=== Version ===		=== Version ===
	0.1.20, 1.6, 1.14, 1.16.1, 1.17		0.1.20, 1.6, 1.13, 1.14, 1.16.1, 1.18, 1.21

	=== Author / Distributor ===		=== Author / Distributor ===

Chelsea: /* Version */

2024-05-14T13:33:44Z

Version

← Older revision		Revision as of 09:33, 14 May 2024
Line 9:		Line 9:

	=== Version ===		=== Version ===
	0.1.20, 1.6, 1.14, 1.16.1		0.1.20, 1.6, 1.14, 1.16.1, 1.17

	=== Author / Distributor ===		=== Author / Distributor ===

Shtsai at 18:39, 5 September 2023

2023-09-05T18:39:58Z

← Older revision		Revision as of 14:39, 5 September 2023
Line 9:		Line 9:

	=== Version ===		=== Version ===
	0.1.20, 1.9, 1.10		0.1.20, 1.6, 1.14, 1.16.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	'''Version 0.1.20'''		'''Version 0.1.20'''

	Installed in /apps/eb/SAMtools/0.1.20-GCC-8.3.0		Installed in /apps/eb/SAMtools/0.1.20-GCC-11.2.0

	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/0.1.20-GCC-8.3.0		ml SAMtools/0.1.20-GCC-11.2.0
	</pre>		</pre>

	'''Version 1.9'''		'''Version 1.6'''

	Installed in /apps/eb/SAMtools/1.9-GCC-8.3.0		Installed in /apps/eb/SAMtools/1.6-GCC-11.2.0

	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/1.9-GCC-8.3.0		ml SAMtools/1.6-GCC-11.2.0
	</pre>		</pre>

	'''Version 1.10'''		'''Version 1.14'''

	Installed in /apps/eb/SAMtools/1.10-GCC-8.3.0		Installed in /apps/eb/SAMtools/1.14-GCC-11.2.0

	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/1.10-GCC-8.3.0		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
			<pre class="gscript">
			ml SAMtools/1.16.1-GCC-11.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SAMtools/1.10-GCC-8.3.0<br>		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/1.10-GCC-8.3.0		ml SAMtools/1.16.1-GCC-1.3.0

	samtools --help		samtools --help

	Program: samtools (Tools for alignments in the SAM format)		Program: samtools (Tools for alignments in the SAM format)
	Version: 1.10 (using htslib 1.10)		Version: 1.16.1 (using htslib 1.16)

	Usage: samtools <command> [options]		Usage: samtools <command> [options]
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	addreplacerg adds or replaces RG tags		addreplacerg adds or replaces RG tags
	markdup mark duplicates		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
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	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
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	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>

Shtsai at 01:49, 28 August 2020

2020-08-28T01:49:55Z

← Older revision		Revision as of 21:49, 27 August 2020
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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 ===
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	=== 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>

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	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>
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	<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]
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	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

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	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
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	-- 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

Shtsai at 18:38, 13 August 2018

2018-08-13T18:38:41Z

@@ Line 9: / Line 9: @@
 === Version ===
-.1.19
+.1.19, 1.3.1, 1.6
 === Author / Distributor ===
@@ Line 21: / Line 21: @@
 === Running Program ===
-The last version of this application is at /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b
+'''Version 0.1.19'''
 To use this version, please load the module with
 <pre class="gscript">
 ml SAMtools/0.1.19-foss-2016b
 </pre>
@@ Line 43: / Line 63: @@
 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>
 </div>
@@ Line 59: / Line 79: @@
 <pre  class="gcommand">
-ml SAMtools/0.1.19-foss-2016b
+ml SAMtools/1.6-foss-2016b
 samtools --help
-[main] unrecognized command '--help'
 </pre>

Yhuang at 18:08, 10 August 2018

2018-08-10T18:08:13Z

← Older revision		Revision as of 14:08, 10 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	1.~~3.1~~		0.1.19

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== 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/1.~~3.1~~-foss-2016b~~-HTSlib-1.3.2~~		The last version of this application is at /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b

	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~~-HTSlib-1.3.2~~		ml SAMtools/0.1.19-foss-2016b
	</pre>		</pre>

Line 43:		Line 43:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SAMtools/1.~~3.1~~-foss-2016b~~-HTSlib-1.3.2~~<br>		ml SAMtools/0.1.19-foss-2016b<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.~~3.1~~-foss-2016b~~-HTSlib-1.3.2~~		ml SAMtools/0.1.19-foss-2016b
	samtools --help		samtools --help
			[main] unrecognized command '--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~~


	</pre>		</pre>

Yhuang at 18:08, 10 August 2018

2018-08-10T18:08:06Z

← Older revision		Revision as of 14:08, 10 August 2018
Line 16:		Line 16:

	=== 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~~"		"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]

Yhuang at 18:07, 10 August 2018

2018-08-10T18:07:58Z

← Older revision		Revision as of 14:07, 10 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	1.6		1.3.1

	=== 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.~~"		"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/1.6-foss-2016b		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/1.6-foss-2016b		ml SAMtools/1.3.1-foss-2016b-HTSlib-1.3.2
	</pre>		</pre>

Line 43:		Line 43:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SAMtools/1.6-foss-2016b<br>		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/1.6-foss-2016b		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: 1.6 (using htslib 1.6)		Version: 1.3.1 (using htslib 1.3.2)

	Usage: samtools <command> [options]		Usage: samtools <command> [options]
Line 80:		Line 80:
	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~~

	-- File operations		-- File operations