Fig 1.
Table 1.
A selection of VCF processing tools included with vcflib (a full list of over 125 tools with full descriptions and options can be found in the online vcflib documentation [17]).
Fig 2.
Example of the VCF format and a VCF transformation to Javascript Object Notation (JSON) using bio-vcf.
(a) the line-based VCF record makes use of separators to split tab-delimited fields into subfields. Subfields are split with characters, =:;/ and so on. This splitting effectively projects a ‘tree-like’ datastructure that can also be represented as (b) a JSON record. JSON is used as a common data exchange format for databases and web-services. This example was generated with (c) the bio-vcf tool using a template [24]. bio-vcf transform data to any textual format, including RDF, HTML, XML etc. See also the bio-vcf section.
Fig 3.
Smoothed pFst (−log10) statistic with color coded number of variants in a window.
As computed by vcflib’s pFst and smoother tools [17].
Fig 4.
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