Summary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDEV)
Category Variant Annotations
OverviewSummarize 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.
GATK version 18.104.22.168-SNAPSHOT built at Mon, 22 Feb 2021 13:44:49 -0800.