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Sequence Alignment/Map Format Speci cation

Sequence Alignment/Map Format SpecificationThe SAM/BAM Format Specification Working Group22 May 2018 The master version of this document can be found printing is version b1ae9f9 from that repository, last modified on the date shown The SAM Format SpecificationSAM stands for Sequence Alignment/Map Format . It is a TAB-delimited text Format consisting of a headersection, which is optional, and an alignment section. If present, the header must be prior to the lines start with @ , while alignment lines do not. each alignment line has 11 mandatory fields foressential alignment information such as mapping position, and variable number of optional fields for flexibleor aligner specific specification is for version of the SAM and BAM formats. each SAM and BAM file mayoptionally specify the version being used via the@HD VNtag. For full version history see Appendix explicitly specified elsewhere, all fields are encoded using 7-bit US-ASCII1in using the POSIX /C locale.

Each header line begins with the character ‘@’ followed by one of the two-letter header record type codes de ned in this section. In the header, each line is TAB-delimited and, apart from @CO lines, each data eld follows a format ‘TAG:VALUE’ where TAG is a two-character string that de nes the format and content of VALUE.

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Transcription of Sequence Alignment/Map Format Speci cation

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The Variant Call Format (VCF) Version 4.1 Specification

samtools.github.io

encouraged to use the rs number(s). No identifier should be present in more than one data record. If there is no identifier available, then the missing value should be used. (String, no whitespace or semicolons permitted) 4. REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted.

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Sequence Alignment/Map Format Specification

samtools.github.io

Template A DNA/RNA sequence part of which is sequenced on a sequencing machine or assembled from raw sequences. Segment A contiguous sequence or subsequence. Read A raw sequence that comes off a sequencing machine. A read may consist of multiple segments. For sequencing data, reads are indexed by the order in which they are sequenced.

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1.2.3 Filter field format FILTERs that have been applied to the data should be described as follows: ##FILTER=<ID=ID,Description="description"> 1.2.4 Individual format field format Likewise, Genotype fields specified in the FORMAT field should be described as follows: ##FORMAT=<ID=ID,Number=number,Type=type,Description="description">

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1.2.7 Contig field format As with chromosomal sequences it is highly recommended (but not required) that the header include tags describing the contigs referred to in the VCF file. This furthermore allows these contigs to come from different files. The format

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Each header line begins with the character ‘@’ followed by one of the two-letter header record type codes defined in this section. In the header, each line is TAB-delimited and, apart from@CO lines, each data field follows a format ‘TAG:VALUE’ where TAG is a two-character string that defines the format and content of VALUE.

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