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