GenotypeSummaries

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

Category Variant Annotations

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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 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.