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See the [SAM File Format Specification](http://samtools.sourceforge.net/SAMv1.pdf) for details about the SAM alignment format.
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By default, *samblaster* reads SAM input from **stdin** and writes SAM to **stdout**. Input SAM file usually contain paired end data (see [Duplicate Identification](#DupIdentification) below), must contain a sequence header, and must be __read-id grouped<sup>1<sup>__.
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By default, *samblaster* reads SAM input from **stdin** and writes SAM to **stdout**. Input SAM files usually contain paired end data (see [Duplicate Identification](#DupIdentification) below), must contain a sequence header, and must be __read-id grouped<sup>1<sup>__.
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By default, the output SAM file will contain all the alignments in the same order as the input, with duplicates marked with SAM FLAG 0x400. The **--removeDups** option will instead remove duplicate alignments from the output file.
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__<sup>1</sup>A read-id grouped__ SAM file is one in which all alignments for a read-id are grouped together in adjacent lines.
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__<sup>1</sup>A read-id grouped__ SAM file is one in which all alignments for a read-id (QNAME) are grouped together in adjacent lines.
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Aligners naturally produce such files.
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They can also be created by sorting a SAM file by read-id.
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But as shown below, sorting the input to *samblaster* by read-id is not required if the alignments are already grouped.
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To take input alignments directly from _bwa mem_ and output to _samtools view_ to compress SAM to BAM:
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```
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bwa mem index samp.r1.fq samp.r2.fq | samblaster | samtools view -Sb - > samp.out.bam
-o --output FILE Output sam file for all input alignments [stdout].
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-e --excludeDups Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file.
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-r --removeDups Remove duplicates reads from all output files. (Implies --excludeDups).
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--addMateTags Add MC and MQ tags to all output paired-end SAM lines.
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--ignoreUnmated Suppress abort on unmated alignments. Use only when sure input is read-id grouped and alignments have been filtered.
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<b>--ignoreUnmated is not recommended for general use. It disables checks that detect incorrectly sorted input.</b>
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-M Compatibility mode (details below); both FLAG 0x100 and 0x800 denote supplemental (chimeric). Similar to <i>bwa mem</i> <b>-M</b> option.
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--maxSplitCount INT Maximum number of split alignments for a read to be included in splitter file. [2]
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--maxUnmappedBases INT Maximum number of un-aligned bases between two alignments to be included in splitter file. [50]
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--minIndelSize INT Minimum structural variant feature size for split alignments to be included in splitter file. [50]
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--minNonOverlap INT Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file. [20]
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--minClipSize INT Minumum number of bases a mapped read must be clipped to be included in unmapped file. [20]
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-h --help Print samblaster help to stderr.
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-q --quiet Output fewer statistics.
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--version Print samblaster version number to stderr.
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```
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</pre>
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---
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**ALIGNMENT TYPE DEFINITIONS:<aname="Definitions"></a>**
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Below, we will use the following definitions for alignment types.
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Starting with *samblaster* release 0.1.22, these definitions are affected by the use of the **-M** option.
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By default, *samblaster* will use the current definitions of alignment types as specified in the [SAM Specification](http://samtools.sourceforge.net/SAMv1.pdf).
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Namely, alignments marked with FLAG 0x100 are considered *secondary*, while those marked with FLAG 0x800 are considered *supplemental*.
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If the **-M** option is specified, alignments marked with either FLAG 0x100 or 0x800 are considered *supplemental*, and no alignments are considered *secondary*.
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A *primary* alignment is always one that is neither *secondary* nor *supplemental*.
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Only *primary* and *supplemental* alignments are used to find chimeric (split-read) mappings.
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The **-M** flag is used for backward compatibility with older SAM/BAM files in which "chimeric" alignments were marked with FLAG 0x100, and should also be used with output from more recent runs of *bwa mem* using its **-M** option.
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1. For pairs in which both reads are mapped, both signatures must match.
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2. For pairs in which only one side is mapped (an "orphan"), the signature of the mapped read must match a previously seen orphan. In an orphan pair, the unmapped read need not appear in the input file. In addition, mapped non-paired single read alignments will be treated the same as an orphan pair with a missing unmapped read.
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3. No doubly unmapped pair will be marked as a duplicate.
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4. Any *secondary*alignment (FLAG 0x100 or 0x800) associated with a duplicate primary alignment will also be marked as a duplicate.
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4. Any *secondary* or *supplemental* alignment associated with a duplicate *primary* alignment will also be marked as a duplicate.
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---
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**DISCORDANT READ PAIR IDENTIFICATION:**
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A **discordant** read pair is one which meets all of the following criteria:
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1. Both side of the read pair are mapped (neither FLAG 0x4 or 0x8 is set).
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2. The *properly paired* FLAG (0x2) is not set.
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3. Secondary alignments (FLAG 0x100 or 0x800) are never output as discordant, although a discordant read pair can have secondary alignments associated with them.
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3.*Secondary*or *supplemental* alignments are never output as discordant, although a discordant read pair can have such alignments associated with them.
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4. Duplicate read pairs that meet the above criteria will be output as discordant unless the **-e** option is used.
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---
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**SPLIT READ IDENTIFICATION:**
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**Split Read** alignments are derived from a single read when one portion of the read aligns to a different region of the reference genome than another portion of the read. Such pairs of alignments often define a structural variant (SV) breakpoint, and are therefore useful input to SV detection algorithms such as [LUMPY](https://github.com/arq5x/lumpy-sv/). *samblaster* uses the following strategy to identify split reads alignments.
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1. Identify reads that have between two and **--maxSplitCount** alignments.
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1. Identify reads that have between two and **--maxSplitCount***primary* and *supplemental*alignments.
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2. Sort these alignments by their strand-normalized position along the read.
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3. Two alignments are output as splitters if they are adjacent on the read, and meet these criteria:
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- each covers at least **--minNonOverlap** base pairs of the read that the other does not.
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---
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**UNMAPPED/CLIPPED READ IDENTIFICATION:**
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An **unmapped** or **clipped** read is one that is unaligned over all or part of its length respectively. The lack of a full alignment may be caused by a SV breakpoint that falls within the read. Therefore, *samblaster* will optionally output such reads to a FASTQ file for re-alignment by a tool, such as [YAHA](http://faculty.virginia.edu/irahall/yaha/), geared toward finding split-read mappings. *samblaster* applies the following strategy to identify and output unmapped/clipped reads:
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An **unmapped** or **clipped** read is a *primary* alignment that is unaligned over all or part of its length respectively. The lack of a full alignment may be caused by a SV breakpoint that falls within the read. Therefore, *samblaster* will optionally output such reads to a FASTQ file for re-alignment by a tool, such as [YAHA](https://github.com/GregoryFaust/yaha/), geared toward finding split-read mappings. *samblaster* applies the following strategy to identify and output unmapped/clipped reads:
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1. An **unmapped** read has the *unmapped read* FLAG set (0x4).
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2. A **clipped** read is a mapped read with a CIGAR string that begins or ends with at least **--minClipSize** unaligned bases (CIGAR code S or H), and is not from a read that has one or more *secondary* alignments (FLAG 0x100).
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2. A **clipped** read is a mapped read with a CIGAR string that begins or ends with at least **--minClipSize** unaligned bases (CIGAR code S and/or H), and is not from a read that has one or more *supplemental* alignments.
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3. In order for *samblaster* to output the entire sequence for clipped reads, the input SAM file must have soft clipped primary alignments.
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4.*samblaster* will output unmapped/clipped reads into a FASTQ file if QUAL information is available in the input file, and a FASTA file if not.
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5. Unmapped/clipped reads that are part of a duplicate read pair will be output unless the **-e** option is used.
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