Mercurial > repos > youngkim > ezbamqc
comparison ezBAMQC/src/htslib/sam.5 @ 0:dfa3745e5fd8
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| author | youngkim |
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| date | Thu, 24 Mar 2016 17:12:52 -0400 |
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| -1:000000000000 | 0:dfa3745e5fd8 |
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| 1 '\" t | |
| 2 .TH sam 5 "August 2013" "htslib" "Bioinformatics formats" | |
| 3 .SH NAME | |
| 4 sam \- Sequence Alignment/Map file format | |
| 5 .\" | |
| 6 .\" Copyright (C) 2009, 2013 Genome Research Ltd. | |
| 7 .\" | |
| 8 .\" Author: Heng Li <lh3@sanger.ac.uk> | |
| 9 .\" | |
| 10 .\" Permission is hereby granted, free of charge, to any person obtaining a | |
| 11 .\" copy of this software and associated documentation files (the "Software"), | |
| 12 .\" to deal in the Software without restriction, including without limitation | |
| 13 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense, | |
| 14 .\" and/or sell copies of the Software, and to permit persons to whom the | |
| 15 .\" Software is furnished to do so, subject to the following conditions: | |
| 16 .\" | |
| 17 .\" The above copyright notice and this permission notice shall be included in | |
| 18 .\" all copies or substantial portions of the Software. | |
| 19 .\" | |
| 20 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 21 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 22 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL | |
| 23 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 24 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | |
| 25 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | |
| 26 .\" DEALINGS IN THE SOFTWARE. | |
| 27 .\" | |
| 28 .SH DESCRIPTION | |
| 29 Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started | |
| 30 with the `@' symbol, each alignment line consists of: | |
| 31 .TS | |
| 32 nlbl. | |
| 33 1 QNAME Query template/pair NAME | |
| 34 2 FLAG bitwise FLAG | |
| 35 3 RNAME Reference sequence NAME | |
| 36 4 POS 1-based leftmost POSition/coordinate of clipped sequence | |
| 37 5 MAPQ MAPping Quality (Phred-scaled) | |
| 38 6 CIGAR extended CIGAR string | |
| 39 7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME) | |
| 40 8 MPOS 1-based Mate POSistion | |
| 41 9 TLEN inferred Template LENgth (insert size) | |
| 42 10 SEQ query SEQuence on the same strand as the reference | |
| 43 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) | |
| 44 12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE | |
| 45 .TE | |
| 46 .PP | |
| 47 Each bit in the FLAG field is defined as: | |
| 48 .TS | |
| 49 lcbl. | |
| 50 0x0001 p the read is paired in sequencing | |
| 51 0x0002 P the read is mapped in a proper pair | |
| 52 0x0004 u the query sequence itself is unmapped | |
| 53 0x0008 U the mate is unmapped | |
| 54 0x0010 r strand of the query (1 for reverse) | |
| 55 0x0020 R strand of the mate | |
| 56 0x0040 1 the read is the first read in a pair | |
| 57 0x0080 2 the read is the second read in a pair | |
| 58 0x0100 s the alignment is not primary | |
| 59 0x0200 f the read fails platform/vendor quality checks | |
| 60 0x0400 d the read is either a PCR or an optical duplicate | |
| 61 0x0800 S the alignment is supplementary | |
| 62 .TE | |
| 63 .P | |
| 64 where the second column gives the string representation of the FLAG field. | |
| 65 .SH SEE ALSO | |
| 66 .TP | |
| 67 https://github.com/samtools/hts-specs | |
| 68 The full SAM/BAM file format specification |