Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

Articles in this section

See more

SampleList Follow

Avatar
GATK Team

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.

Return to top

GATK version 4.2.6.1-SNAPSHOT built at Wed, 13 Apr 2022 13:12:10 -0700.

Related articles

0 comments

Please sign in to leave a comment.

Powered by Zendesk