GC content of the reference around the given site
INFO=<ID=GC,Number=1,Type=Float,Description="GC content around the variant (see docs for window size details)">
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. Some sequencing technologies have trouble with high GC content because of the stronger bonds of G-C nucleotide pairs, so high GC values tend to be associated with low coverage depth and lower confidence calls.
The window size used to calculate the GC content around the site is determined by the tool used for annotation (UnifiedGenotyper, HaplotypeCaller or VariantAnnotator). See the Tool Documentation for each of these tools to find out what window size they use.
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.