Sequence Alignment/Map Format Specification
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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Sequence Alignment/Map Format Speci cation
samtools.github.io1.3 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.
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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