GC content of the reference around the given site

Category Variant Annotations

VCF Field INFO (variant-level)


The GC content is the number of GC bases relative to the total number of bases (# GC bases / # all bases) around this site on the reference.


The window size used to calculate the GC content around the site is set by the tool used for annotation (currently UnifiedGenotyper, HaplotypeCaller or VariantAnnotator). See the Technical Document for each tool to find out what window size they use.

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA