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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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Algorithms

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  • Structural variant (SV) discovery
    In this article, you'll learn how to identify structural variants in one or m...
  • ActiveRegion determination (HaplotypeCaller and Mutect2)
    This document details the procedure used by HaplotypeCaller to define ActiveR...
  • Evaluating the evidence for haplotypes and variant alleles (HaplotypeCaller and Mutect2)
    This document details the procedure used by HaplotypeCaller to evaluate the e...
  • Local re-assembly and haplotype determination (HaplotypeCaller and Mutect2)
    This document details the procedure used by HaplotypeCaller to re-assemble re...
  • Allele-specific annotation and filtering of germline short variants
    Overview The traditional VQSR recalibration paradigm evaluates each position...
  • Variant Quality Score Recalibration (VQSR)
    VQSR stands for Variant Quality Score Recalibration. In a nutshell, it is a s...
  • Evaluating the quality of a germline short variant callset
    The germline short variant discovery pipeline produces a variant callset in t...
  • HaplotypeCaller Reference Confidence Model (GVCF mode)
    This document describes the reference confidence model applied by HaplotypeCa...
  • Base Quality Score Recalibration (BQSR)
    BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data...
  • After gCNV calling considerations
    The Germline CNV (gCNV) workflow tutorial is available here. The tutorial lay...
  • Assigning per-sample genotypes (HaplotypeCaller)
    This document describes the procedure used by HaplotypeCaller to assign genot...
  • Genotype Refinement workflow for germline short variants
    Contents Overview Summary of workflow steps Output annotations Example More...
  • Somatic calling is NOT simply a difference between two callsets
    To better understand what somatic calling entails, we contrast it to germline...
  • HaplotypeCaller in a nutshell
    This document outlines the basic operation of the HaplotypeCaller run in its ...
  • Difference between QUAL and GQ annotations in germline variant calling
    It seems people often get confused about the difference between QUAL and GQ, ...
  • Hard-filtering germline short variants
    This document aims to provide some insight into the logic of the generic hard...
  • Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs
    PL is a sample-level annotation calculated by HaplotypeCaller and GenotypeGVC...
  • The logic of joint calling for germline short variants
    Better together For germline short variants (SNPs and indels), we recommend ...
  • Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
    This document describes the new approach to joint variant discovery that is a...

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