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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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AS_InbreedingCoeff Follow

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GATK Team
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Allele-specific likelihood-based test for the consanguinity among samples (AS_InbreedingCoeff)

Category Variant Annotations

Overview

Allele-specific likelihood-based test for the inbreeding among samples

This annotation estimates whether there is evidence of inbreeding in a population. The higher the score, the higher the chance that there is inbreeding.

Statistical notes

The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is the F statistic from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.

Caveats

  • The inbreeding coefficient can only be calculated for cohorts containing at least 10 founder samples.
  • This annotation can take a valid pedigree file to specify founders. If not specified, all samples will be considered as founders.

Related annotations

  • InbreedingCoeff outputs a version of this annotation that includes all alternate alleles in a single calculation.
  • ExcessHet estimates excess heterozygosity in a population of samples.

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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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