VariantCallingDetailMetrics

Metrics

Category Metrics

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Overview

A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.

This table summarizes the values that are specific to this metric.

Metric	Summary
SAMPLE_ALIAS	The name of the sample being assayed
HET_HOMVAR_RATIO	(count of hets)/(count of homozygous non-ref) for this sample
PCT_GQ0_VARIANTS	The percentage of variants in a particular sample that have a GQ score of 0.
TOTAL_GQ0_VARIANTS	The total number of variants in a particular sample that have a GQ score of 0.
TOTAL_HET_DEPTH	total number of reads (from AD field) for passing bi-allelic SNP hets for this sample

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