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About the GATK Best Practices
This document provides important context information about how the GATK Best Practices are developed and what are their limitations. Contents What are the GATK Best Practices? Analysis phases ...
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(How to) Run GATK in a Docker container
This document explains how to install and use Docker to run GATK on a local machine. For a primer on what Docker containers are for and related terminology, see this Dictionary entry. Contents ...
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Hard-filtering germline short variants
This document aims to provide some insight into the logic of the generic hard-filtering recommendations that we provide as a substitute for VQSR (the method we normally recommend for filtering germ...
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Getting started with GATK4
GATK — properly pronounced "Gee-ay-tee-kay" (/dʒi•eɪ•ti•keɪ/) and not "Gat-kay" (/ɡæt•keɪ/) — stands for Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-through...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencing machine when it estimates the accuracy of eac...
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The logic of joint calling for germline short variants
Better together For germline short variants (SNPs and indels), we recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices...
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Biallelic vs Multiallelic sites
A biallelic site is a specific locus in a genome that contains two observed alleles, counting the reference as one, and therefore allowing for one variant allele. In practical terms, this is what y...
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Human genome reference builds - GRCh38 or hg38 - b37 - hg19
This document covers the specifics of human genome reference assemblies. For more general information about reference genomes, including definitions of specialize terms used here, please see the Gl...
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GATK4 command-line syntax
Contents Java command basics Using the gatk wrapper script (recommended) Adding GATK arguments Adding Java arguments Adding Spark arguments Examples of real commands 1. Java command basics G...
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Spanning or overlapping deletions (* allele)
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at an...