FAQ
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Which training sets arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend... -
FAQ for Mutect2
Here is a collection of questions related to Mutect2 that we frequently find ... -
What is physical phasing?
In the format field of a PGT (Pre-Implantation Genetic Testing) VCF, you may ... -
Where can I get the GATK source code? Is it open-source?
YES! Starting with GATK4 it is fully open-source under a BSD 3-clause license... -
Are there Best Practices for calling variants in RNAseq data?
We are working on updating our recommended workflow for calling variants in R... -
Does GATK work on non-diploid organisms?
YES! In general most GATK tools don't care about ploidy. The major exception... -
How should I cite GATK in my own publications?
To date, we have published three papers on GATK, a preprint in bioRxiv (citat... -
Where can I find known variants, training and truth sets, and other resource files?
For general definitions of these terms, see this Dictionary entry. Humans I... -
How can I make GATK tools run faster?
It sure seems like everyone has a need for speed these days. So, there are tw... -
How can I attend or host a GATK workshop?
The list of upcoming workshops is available in the Events calendar. The cou... -
When should I restrict my analysis to specific intervals?
This document covers the reasoning behind the use of genomic intervals. If yo... -
What are the requirements for running GATK?
Contents Skills Input data Software Hardware 1. Skills / experience W... -
How should I prepare for a GATK workshop?
So you're going to a GATK workshop? Fantastic! We're looking forward to guidi... -
Can I get a notification when my question is answered or commented on?
Yes, absolutely! By default, the site will send notifications about replies ... -
Can I use different versions of the GATK at different steps of my analysis?
Short answer: NO, unless it's a combo that we made. Medium answer: No, at le... -
How should I pre-process data from multiplexed sequencing and multi-library designs?
Our Best Practices pre-processing documentation assumes a simple experimental... -
What input files does the GATK accept or require?
Analyses done with the GATK typically involve several (though not necessarily... -
What types of variants can GATK tools detect or handle?
The answer depends on what tool we're talking about, and whether we're consid...