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Sequence Alignment/Map Format Specification

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.

coordinate system. 0-based coordinate system A coordinate system where the first base of a sequence is zero. In this coordinate system, a region is specified by a half-closed-half-open interval. For example, the region between the 3rd and the 7th bases inclusive is [2,7). The BAM, BCFv2, BED, and PSL formats are using the 0-based coordinate system.

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Transcription of Sequence Alignment/Map Format Specification

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Sequence Alignment/Map Format Speci cation

samtools.github.io

1.3 The header section Each header line begins with the character ‘@’ followed by one of the two-letter header record type codes de ned in this section.

  Format

The Variant Call Format (VCF) Version 4.2 Specification

samtools.github.io

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">

  Descriptions

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.

  Reference

The Variant Call Format (VCF) Version 4.2 Specification

samtools.github.io

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

  Contig

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