Sequence Alignment/Map Format Speci cation
Sequence Alignment/Map Format Speci cation The SAM/BAM Format Speci cation Working Group 22 May 2018 The master version of this document can be found at https://github.com/samtools/hts-specs.
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Sequence Alignment/Map Format Specification
samtools.github.ioTemplate 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.
The Variant Call Format (VCF) Version 4.2 Specification
samtools.github.io1.2.3 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">
The Variant Call Format (VCF) Version 4.1 Specification
samtools.github.ioencouraged 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.
The Variant Call Format (VCF) Version 4.2 Specification
samtools.github.io1.2.7 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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