69 lines
2.7 KiB
Groff
69 lines
2.7 KiB
Groff
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'\" t
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.TH sam 5 "August 2013" "htslib" "Bioinformatics formats"
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.SH NAME
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sam \- Sequence Alignment/Map file format
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.\"
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.\" Copyright (C) 2009, 2013-2014 Genome Research Ltd.
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.\"
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.\" Author: Heng Li <lh3@sanger.ac.uk>
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.\"
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.\" Permission is hereby granted, free of charge, to any person obtaining a
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.\" copy of this software and associated documentation files (the "Software"),
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.\" to deal in the Software without restriction, including without limitation
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.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
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.\" and/or sell copies of the Software, and to permit persons to whom the
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.\" Software is furnished to do so, subject to the following conditions:
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.\"
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.\" The above copyright notice and this permission notice shall be included in
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.\" all copies or substantial portions of the Software.
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.\"
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.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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.\" DEALINGS IN THE SOFTWARE.
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.\"
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.SH DESCRIPTION
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Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started
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with the `@' symbol, each alignment line consists of:
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.TS
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nlbl.
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1 QNAME Query template/pair NAME
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2 FLAG bitwise FLAG
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3 RNAME Reference sequence NAME
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4 POS 1-based leftmost POSition/coordinate of clipped sequence
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5 MAPQ MAPping Quality (Phred-scaled)
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6 CIGAR extended CIGAR string
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7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
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8 MPOS 1-based Mate POSition
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9 TLEN inferred Template LENgth (insert size)
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10 SEQ query SEQuence on the same strand as the reference
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11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
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12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE
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.TE
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.PP
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Each bit in the FLAG field is defined as:
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.TS
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lcbl.
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0x0001 p the read is paired in sequencing
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0x0002 P the read is mapped in a proper pair
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0x0004 u the query sequence itself is unmapped
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0x0008 U the mate is unmapped
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0x0010 r strand of the query (1 for reverse)
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0x0020 R strand of the mate
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0x0040 1 the read is the first read in a pair
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0x0080 2 the read is the second read in a pair
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0x0100 s the alignment is not primary
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0x0200 f the read fails platform/vendor quality checks
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0x0400 d the read is either a PCR or an optical duplicate
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0x0800 S the alignment is supplementary
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.TE
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.P
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where the second column gives the string representation of the FLAG field.
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.SH SEE ALSO
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.TP
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https://github.com/samtools/hts-specs
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The full SAM/BAM file format specification
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