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Summarize genotype statistics from all samples at the site level

Category Annotation Modules

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples">
  • INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values">
  • INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values">

  • Overview

    This annotation collects several genotype-level statistics from all samples and summarizes them in the INFO field. The following statistics are collected:

    • Number of called chromosomes (should amount to ploidy * called samples)
    • Number of no-called samples
    • p-value from Hardy-Weinberg Equilibrium test
    • Mean of all GQ values
    • Standard deviation of all GQ values


    These summaries can all be recomputed from the genotypes on the fly but it is a lot faster to add them here as INFO field annotations.

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.