Samtools - Revision history

Rf at 13:45, 15 June 2017

2017-06-15T13:45:43Z

2017-06-15T13:45:26Z

2017-04-28T16:51:54Z

2017-04-26T14:09:58Z

2017-04-05T14:03:32Z

2017-03-13T16:51:40Z

2017-03-13T15:07:32Z

2017-03-02T14:09:26Z

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2017-02-15T14:14:47Z

@@ Line 176: / Line 176: @@
 * [http://biobits.org/samtools_primer.html Ethan Cerami's Primer]
 * [http://www.htslib.org/doc/samtools.html samtools' manual page]
-* [http://www.samformat.info/sam-format-flag meaning of the FLAG vlaue from samformat.info]
+* [http://www.samformat.info/sam-format-flag meaning of the FLAG value from samformat.info]
 = Installation Notes =
 Since version 1.2, samtools build structure has changed. Before it was monolithic, since 1.2 it is split into a library, htslib and smatools proper. A third package, bcftools, is often mentioned in the same breath, though

@@ Line 176: / Line 176: @@
 * [http://biobits.org/samtools_primer.html Ethan Cerami's Primer]
 * [http://www.htslib.org/doc/samtools.html samtools' manual page]
 = Installation Notes =
 Since version 1.2, samtools build structure has changed. Before it was monolithic, since 1.2 it is split into a library, htslib and smatools proper. A third package, bcftools, is often mentioned in the same breath, though

@@ Line 33: / Line 33: @@
 # samtools commands follow the subcommand style: i.e. they always start with a "samtools" followed by subcommand (eg. "sort", "view", etc) which identify the exact operation samtools will perform. This is due to the fact that samtools is a suite of tools for handling alignment files in sam/bam format.
 # Two input files will commonly be needed, often a sam/bam file and also the reference file.
-# '''view''' is a commonly used subcommand, whose name however refers to internal viewing, because external user visuals is not samtools strong point, though it has some capabilities in this regard ("tview").
+# '''view''' is the commonly used subcommand, which itself has a number of extra option and the name however might refer to internal viewing, because external user visuals is not samtools strong point, though it has some capabilities in this regard ("tview").
 = Common commands =
@@ Line 78: / Line 120: @@
 When '''view''' is used, it outputs headerless apparently. You can stop this with the '''-h'''.
 == tview ==

@@ Line 55: / Line 55: @@
 to see if you can find the right reference file.
-Once you have a bam file, it's usual to quickly proceed to sorting and then indexing (for which sorting is necessary) because many tools that will typically be run afterwards, require it. Sorting is often as easy as the following, and this is typically the command-line you'll need:
+Once you have a bam file, it's usual to quickly proceed to sorting and then indexing (for which sorting is necessary) because many tools that will typically be run afterwards, require it. Sorting is often as easy as the following, and this is typically the command-line you'll need if you're on '''version 0.1.19''' or earlier:
   samtools sort aln.bam aln_sorted
-One thing to note here is that samtools sort will automatically add a bam extension to the second argument. In more modern version of samtools, you need the -o, as in:
+Note here how the sot subcommand automatically add a '''bam''' extension to the second argument. In '''versions 1.x.x''' i.e. more modern versions, of samtools, you need the -o, as in:
   samtools sort aln.bam -o aln_sorted.bam
 Indexing is quite quick, and also seems to generate the index file (which appends a .bai extension) in the subdirectory where the bams are found. So, the following command:

@@ Line 59: / Line 59: @@
   samtools sort aln.bam aln_sorted
-One thing to note here is that samtools sort will automatically add a bam extension to the second argument.
+One thing to note here is that samtools sort will automatically add a bam extension to the second argument. In more modern version of samtools, you need the -o, as in:
 Indexing is quite quick, and also seems to generate the index file (which appends a .bai extension) in the subdirectory where the bams are found. So, the following command:

@@ Line 46: / Line 46: @@
 * '''-b''', refers to the output being BAM.
 * '''-o''', does not refer to "output name" like it usually might, it refers to STDOUT. This is for piping convenience.
-* '''-h''', is for making sure the header is passed to the bam.
+* '''-h''', is for making sure the header is passed to the bam. Without this option, the default of "noheader" is in force.
 * note that the bam extension will '''not''' be added automatically. You need to give the name plus extension after the -o switch. Note that the '''sort''' subcommand does do this however.

@@ Line 37: / Line 37: @@
 = Common commands =
-A '''bam''' file is the compressed binary version of a '''sam''' file. It exists purely for efficiency purposes and contains the same information. Because it is not human-readable, converting out of, but also back into bam, is very frequent activity. It is done via the '''view''' subcommand in the following canonical way fo converting from sam to bam:
+A '''bam''' file is the compressed binary version of a '''sam''' file. It exists purely for efficiency purposes and contains the same information. Because it is not human-readable, converting out of, but also back into bam, is very frequent activity. It is done via the '''view''' subcommand in the following canonical way of converting from sam to bam, and it needs to be redirected into bam filename:
-  samtools view -S -h -b <your_chosen_bam_filename> > <input_sam_filename>
+  samtools view -S -h -b input_sam_filename > your_chosen_bam_filename
 <u>Explanation:</u>

← Older revision		Revision as of 14:14, 15 February 2017
Line 104:		Line 104:

	bcftools view -v -c -g samtools_bowtie/SRR030257.bcf > samtools_bowtie/SRR030257.vcf		bcftools view -v -c -g samtools_bowtie/SRR030257.bcf > samtools_bowtie/SRR030257.vcf
		+
		+	== merge ==
		+
		+	Samtools does indeed have a merge subcommand but it is unpopular. Practitioners generally use picard tools instead. This has to do with '''merge''' not establishing a read-grup or @RG for each component bam file.

	= Functionality relating to SAM format =		= Functionality relating to SAM format =