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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List of samples that are not homozygous reference at a variant site (Samples)

Category Variant Annotations

Overview

List samples that are non-reference at a given variant site

The output is a list of the samples that are genotyped as having one or more variant alleles. This allows you to easily determine which samples are non-reference (heterozygous or homozygous-variant) and compare them to samples that are homozygous-reference. This annotation is particularly useful for large cohorts where the genotype fields are difficult to manually match with sample names.

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GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.

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