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HaplotypeCaller

Definition
AI-generated

HaplotypeCaller is a GATK tool that calls germline SNVs and indels from aligned reads using local reassembly and haplotype likelihoods.

Topics
Sequencing Data Analysis Bioinformatics
URL
https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-HaplotypeCaller
Related
Genomic Variant Call Format (gVCF) Genome Analysis Toolkit (GATK) GenomicsDB

Why it matters in GWAS

Short-read WGS and WES pipelines in published GWAS often name HaplotypeCaller as the primary variant caller; understanding it separates caller-specific behavior (indels, active regions, gVCF) from downstream association modeling.

Example usage

"Single-sample gVCFs were produced with HaplotypeCaller in GVCF mode, then jointly genotyped with GenomicsDBImport and GenotypeGVCFs."

Genomic Variant Call Format (gVCF) Genome Analysis Toolkit (GATK) GenomicsDB Indel Joint genotyping Parabricks Variant Calling
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • DePristo MA, et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics. https://doi.org/10.1038/ng.806
  • Poplin R, et al. (2018). Scaling accurate genetic variant discovery to tens of thousands of samples. Nature. https://doi.org/10.1038/nature24239
← Haplotype Haplotype Reference Consortium (HRC) →

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