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GenotypeSummaries

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

Category Variant Annotations


Overview

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

Note

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 4.0.4.0 built at 23-40-2018 11:40:56.