What do GATK workshops cover?
This is a summary description of our standard 3-day workshop, with optional 1-day pipelining add-on at the discretion of the organizer. Overview This workshop formula focuses on the core steps involved...
View ArticleHow should I select samples for a Panel of Normals for somatic analysis?
The Panel of Normals (PoN) plays two important roles in somatic variant analysis: Exclude germline variant sites that are found in the normals to avoid calling them as potential somatic variants in the...
View ArticleCan I apply the germline variant joint calling workflow to my RNAseq data?
We have not yet validated the joint genotyping methods (HaplotypeCaller in -ERC GVCF mode per-sample then GenotypeGVCFs per-cohort) on RNAseq data. Our standard recommendation is to process RNAseq...
View ArticleWhat's in the resource bundle and how can I get it?
1. Obtaining the bundle Inside of the Broad, the latest bundle will always be available in: /humgen/gsa-hpprojects/GATK/bundle/current with a subdirectory containing for each reference sequence and...
View ArticleWhich training sets / arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based on...
View ArticleHow can I prepare a FASTA file to use as reference?
This article describes the steps necessary to prepare your reference file (if it's not one that you got from us). As a complement to this article, see the relevant tutorial. Why these steps are...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleShould I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?
Use HaplotypeCaller! The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, its ability to call...
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How can I run different versions of Java on the same computer?
We sometimes need to be able to use multiple versions of Java on the same computer to run command-line tools that have different version requirements. At the time of writing, GATK requires an older...
View ArticleCollected FAQs about interval lists
1. What file formats do you support for interval lists? We support three types of interval lists, as mentioned here. Interval lists should preferentially be formatted as Picard-style interval lists,...
View ArticleHow should I pre-process data from multiplexed sequencing and multi-library...
Our Best Practices Pre-processing documentation assumes a simple experimental design in which you have one set of input sequence files (forward/reverse or interleaved FASTQ, or unmapped uBAM) per...
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What is a VCF and how should I interpret it?
This document describes "regular" VCF files. For information on the special kind of VCF called gVCF, produced by HaplotypeCaller in -ERC GVCF mode, please see this companion document. Contents What is...
View ArticleWhat is the difference between QUAL and GQ annotations?
There has been a lot of confusion about the difference between QUAL and GQ, and we hope this FAQ will clarify the difference. The basic difference is that QUAL refers to the variant site whereas GQ...
View ArticleLane, Library, Sample and Cohort -- what do they mean and why are they...
There are four major organizational units for next-generation DNA sequencing processes that used throughout the GATK documentation: Lane: The basic machine unit for sequencing. The lane reflects the...
View ArticleI have multiple read groups for 1 sample. How should I pre-process them?
Things can get a bit messy when you have multiple libraries (or read groups) for a sample. You may not know how to organize the data for the pre-processing steps or how to feed the data into Haplotype...
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Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
View ArticleHow can I access the GSA public FTP server?
We make various files available for public download from the GSA FTP server, such as the GATK resource bundle and presentation slides. We also maintain a public upload feature for processing bug...
View ArticleWhat should I use as known variants/sites for running tool X?
1. Notes on known sites Why are they important? Each tool uses known sites differently, but what is common to all is that they use them to help distinguish true variants from false positives, which is...
View ArticleHow should I cite GATK in my own publications?
To date we have published three papers on GATK (citation details below). The ideal way to cite the GATK is to use all as a triple citation, as in: We sequenced 10 samples on 10 lanes on an Illumina...
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
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