GC content of the reference around the given site

Category Variant Annotations

VCF Field INFO (variant-level)

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  • Overview

    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.

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    See also Guide Index | Tool Documentation Index | Support Forum

    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA