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Summary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDEV)

Category Variant Annotations


Summarize genotype statistics from all samples at the site level

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 built at Wed, 30 Jan 2019 10:21:04 +0530.