Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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Metrics

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Overview

Class for holding metrics on a single fingerprint. Note: this is distinct from FingerprintingDetailMetrics and FingerprintingSummaryMetrics in that it is calculated on a single fingerprint, and attempts to describe how likely that fingerprint is to have arisen from an actual sample as opposed to having artifacts such as contamination, or strong bias towards homozygous genotypes. Several tests use "expected" genotype distribution based on the allele frequency stored in the haplotype-database file that is used, and assuming Hardy-Weinberg equilibrium. Please see the FingerprintMetrics definitions http://broadinstitute.github.io/picard/picard-metric-definitions.html#FingerprintMetrics " + for a complete description of the metrics produced by this tool.

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GATK version 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.

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