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About the GATK Best Practices
Data preprocessing for variant discovery
Germline copy number variant discovery CNVs
Germline short variant discovery SNPs Indels
Pipeline Index
RNAseq short variant discovery SNPs Indels
Somatic copy number variant discovery CNVs
Somatic short variant discovery SNVs Indels
Blogs
001. Catching up with the times GATK is moving to a new web home
002. GATK WDL Cromwell and Terra at ASHG 2019
003. Enter the DRAGENGATK
004. Introducing a new forum support policy
005. March 2019 workshop videos on YouTube
006. Learn GATK through workshop tutorials
007. From Python Magic to embedded IGV A closer look at GATK tutorial notebooks
008. The future of GATK tutorials is written in Jupyter Notebooks
009. Test drive GATK Best Practices workflows on Terra
010. Getting started with GATK Terra can make it easier
011. Love to write hate our docs Join our Education team
012. Whats new with Mutect2 since v4110
013. Hacking a community resource prototype for synthetic data
014. An exercise in reproducibility and frustration
015. Fake your data for Science
016. Workshop season is right around the corner
017. Goodbye note to the GATK community
018. New Mutect2 for Liquid Biopsy
019. New Mitochondrial Analysis with Mutect2
020. Improvements in Germline Short Variants Calling Part 2
021. Improvements in Germline Short Variants Calling Part 1
022. Funcotator Functional annotation out of beta
023. Short Variant Caller Roundup
024. CNN deep learning pipeline out of beta
025. Copy Number Variation pipelines out of beta
026. Spark Improvements in 41 Delivering results faster
027. New Features and Improvements in Mutect2
028. GATK 4100 Release
029. New year new Comms team members
030. CrossSpecies Contamination Identification with PathSeq
031. Spam issue on the forum
032. Goodbye GATK Forum
033. Upcoming workshops JuneJulySeptember 2018
034. What is this Machine Learning thing anyway
035. Springtime of GATK4 pipelines and machine learning at BioIT
036. A heck of a way to mark DNA Day
037. Let the 2018 GATK workshop season begin
038. Run the germline GATK Best Practices Pipeline for 5 per genome
039. Batch effects begone Introducing the Functional Equivalence data processing pipeline spec
040. Mutect2 resources guide
041. Offlabel workflow to simply call differences in two samples
042. 7813 downloads of GATK 40 and counting
043. Watch the GATK4 launch event recording on YouTube
044. Version highlights for GATK version 40
045. GATK4 livestream launch event Tuesday 9 Jan detailed agenda and speaker lineup
046. Heads up documentation and website updates for GATK4
047. Scaling up joint calling with GenomicsDB
048. Get free credits worth 250 for running GATK4 pipelines in the cloud
049. Deep learning in GATK4
050. Save the date online event January 9 for the GATK 40 release
051. 9 Things Youve Been Dying To Know About The HaplotypeCaller Paper
052. What is truth Or how an accident of nature can illuminate our path
053. Differences between GATK3 MuTect2 and GATK4 Mutect2
054. Why is HaplotypeCaller slower in the most recent GATK4 beta versions
055. 40 days to GATK 40
056. Service note forum on break support resumes Nov 27
057. IMPORTANT Bug alert for GATK4 GenomicsDBImport
058. Spam issues on the forum
059. Presentation slides and tutorial materials Pretoria 2017
060. Do you use GATK Take this survey win a prize
061. GATK 40 will be released Jan 9 2018
062. GATK events update for Fall 2017 ASHG and more
063. Version highlights for GATK version 38
064. Release notes for GATK version 38
065. Upcoming GATK events in July UK workshops and BOSC 17
066. GATK4 is completely open source
067. Unboxing GATK4
068. GATK4 at BioIT Luncheon with Intel and QampA sessions
069. Conference proceedings Sheilas experience at AGBT 2017
070. A dog a ship and an algorithm that measures relatedness
071. Posters on somatic analysis with GATK4 presented at AACR 2017
072. New interactive support feature in GATK4
073. Help us help you a note to those asking questions
074. 2017 Feb workshop presentation slides and tutorial materials
075. Support team appreciation day say hi and get a prize
076. How long does it take Part 2
077. Version highlights for GATK version 37
078. Release notes for GATK version 37
079. Can a biochemist with one Python course under her belt start running analyses in the cloud
080. Attend or host a GATK workshop to see whats cooking
081. WDL building blocks A tour of resources for pipelining with WDL
082. Were officially BFFs with Intel now
083. 2016 Nov BroadE workshop presentation slides
084. ASHG 2016 in Vancouver Terrible weather exciting science
085. Get ready for ASHG 2016
086. Presentation slides and tutorial materials Basel 2016
087. Soliciting developer feedback on plans to merge Picard GATK4
088. 9 Takeaways to help you get started with GRCh38
089. Upcoming GATK workshop September 2628 in Basel Switzerland
090. Going public with pipeline scripts
091. Interactive map of the global GATK user community
092. Service note we are now softwarebroadinstituteorggatk
093. Service note Important website updates
094. Changing workflows around calling SNPs and indels
095. Presentation slides and tutorial materials Cambridge and Helsinki 2016
096. GATK by the numbers
097. Version highlights for GATK version 36
098. Release notes for GATK version 36
099. Job openings for a Data Scientist and an Associate Software Engineer
100. Notes on differences in GATK 35 test results between Java 7 to 8
101. XHMM support is no longer available here
102. Sneak preview of the GATK release calendar for 2016
103. The doctor is in diagnosing sick SAMBAM files
104. Lets please stop calling it NGS
105. UK April 1415 Workshop Slides
106. Service note expecting forum downtime on May 14th
107. Making GATK available on the cloud for everyone
108. Wrap your head around the Cloud
109. The Art of the Pipeline Introducing Cromwell WDL
110. Metrics say percent Doublecheck those decimals Fractions everywhere
111. How long does it take to run the GATK Best Practices
112. Workshop presentation slides and tutorial materials UCLA 2016
113. Picard Leaps Into the Future
114. I Can See Clearly Now My Variants are Tabled
115. Ahoy mates be ye unmapped
116. What ArrayIndexOutOfBoundsException means and what to do about it
117. Sam flags down a boat
118. GATK Workshops World Tour 2016
119. Beers on Birney
120. Presentation slides for GATK workshops in Australia Feb 14
121. Welcome to the Year of Trying New Things blogging edition
122. Introducing the 2016 GATK support team
123. Holiday Notice Forum unattended during winter break until 1416
124. Away workshop Gent 2015 Dec 8 Variant discovery in RNAseq with GATK
125. US Holiday notice service resumes Nov 30
126. Version highlights for GATK version 35
127. Release notes for GATK version 35
128. 2015 Nov BroadE workshop presentation slides
129. 2015 Nov BroadE workshop handson tutorial materials
130. Registration is now live for the BroadE GATK workshop of Nov 1819 2015
131. Upcoming GATK workshops at Broad and abroad
132. MPG Primer on sequencing and variant discovery pipelines
133. ASHG 2015 Poster Run smarter not harder
134. Countdown to ASHG 2015
135. GATK workshop at ASHG 2015
136. Were hiring It must be Monday
137. New patch version 3446 released
138. Broad Institute and Google Genomics launch GATK as a Service
139. Workshop presentations 2015 Pretoria South Africa 62226
140. Website down for server maintenance over the weekend
141. Update to the accelerated PairHMM library for IBM POWER8 systems
142. Holiday notice forum on hiatus service resumes May 26
143. Version highlights for GATK version 34
144. Release notes for GATK version 34
145. Workshop presentations 2015 UK 42024
146. GATK licensing through Broad starts today
147. The GATK support team is hiring
148. GATK and MuTect licensing moves to directthroughBroad model
149. Workshop presentations 2015 BroadE 319
150. Consolidating GATK Picard tools support
151. Registration open for GATK workshop March 1920
152. Snowpocalypse Part Eleventy
153. GATK in the UK April 2024 workshops
154. Surviving the Snowpocalypse
155. Happy New Year 2015 and welcome back to the GATK forum
156. Happy holidays and see you next year
157. Best Practices VQSR parameters updated
158. Lets play GATK Survivor what tools will get voted off the island
159. New job opening in cancer analysis parttime
160. Speed up HaplotypeCaller on IBM POWER8 systems
161. New Picard version 1124 changes how Picard tools are invoked
162. Appistry webinar about comparing versions of GATK
163. Version highlights for GATK version 33
164. Release notes for GATK version 33
165. A new workflow for refining genotype calls
166. GATK at ASHG 2014
167. The search box is fixed
168. New doc for newbies GATK command syntax
169. New doc for developers regarding sting gt gatk renaming in 32
170. Workshop presentations Philadelphia 918
171. Genome Science UK 2014 my presentation slides and a few impressions
172. Minor license text updates for GATK 3x
173. Calling all GATKsavvy developers were hiring
174. Workshop announcement Philadelphia September 1819
175. Any ploidy goes
176. Appistry webinar on RNAseq analysis pipeline 821
177. Abstract for Genome Science UK Oxford Sept 13
178. Version highlights for GATK version 32
179. Appistry Pipeline Contest
180. Release notes for GATK version 32
181. Meetings workshops conferences oh my carbon footprint
182. Slides from the June 2014 GATK workshop in Brussels Belgium
183. Documentation error in RNAseq workflow
184. GATK workshop in Brussels Belgium June 2426 2014
185. Important notice for GATK versions 26 and older
186. Taking a break over Memorial Day weekend
187. Developer interview Mauricio Carneiro on the raison detre of the GATK
188. New job opening help us write papers about GATK
189. Bug Bulletin AD swapping by SelectVariants with nt in 2x versions
190. Slides from the 410 webinar on GATK 3 features
191. Special webinar on GATK 3 features 410
192. New team member to help with GATK Cancer Tools outreach support
193. Version highlights for GATK version 31
194. Broad collaboration with Intel Bio Team
195. Version highlights for GATK release 30
196. Release notes for GATK version 31
197. Forum support going on hiatus resumes March 17th
198. The GATK reference model pipeline for incremental joint discovery in full detail
199. The GATK Best Practices for variant calling on RNAseq in full detail
200. Release notes for GATK version 30
201. ReduceReads will no longer be in GATK 30
202. Slides from the GATK workshop in Bangkok 36 Mar 2014
203. Scottish National Party obviously
204. GATK 30 Features Overview
205. Blame the weather
206. Get it straight from the horses mouth
207. Poster Teaser The Features of GATK 30
208. Sneak Preview The Spirit of GATK 30
209. Introducing the GATK blog
210. Presentation videos from Best Practices amp Queue workshop Oct 2013
211. Version highlights for GATK release 28
212. Happy holidays Broad on vacation until Jan 2
213. Release notes for GATK version 28
214. Appistry webinar on Broad Tools GATK Cancer Genome Suite
215. Appistry webinar about GATK commercialization
216. Presentation slides for the Oct 2013 workshop are online
217. Bug in VariantsToBinaryPED
218. Appistry webinar on analyzing and annotating cancer genomes
219. Job opportunity for a computational biologist
220. Leadership change in GSA
221. Registration open for the GATK workshop Oct 2122
222. The new Best Practices section is online
223. Version highlights for GATK release 27
224. Release notes for GATK version 27
225. Save the date Next GATK Workshop will be Oct 2122 2013
226. Job opportunity for a computational biologist
227. Appistry webinar on using GATK MuTect for somatic mutations
228. Do you use GATK on RNAseq data
229. Slides from July 2013 workshop
230. Tutorial materials July 2013
231. Spam issues on the GATK forum
232. Version highlights for GATK release 26
233. Workshop registration is OPEN
234. Release notes for GATK version 26
235. New User Story Securing a genetic diagnosis for two children with central hypothyroidism
236. Upcoming GATK workshop preliminary announcement
237. Version highlights for GATK release 25
238. Release notes for GATK version 25
239. Webinar on GATK Best Practices by Appistry open to all
240. Bug in various tools 247 ArrayIndexOutOfBoundsException
241. DepthOfCoverage and DiagnoseTargets our plans for development and support
242. Bug in HaplotypeCaller 247 Bad likelihoods detected
243. Bug in HaplotypeCaller v24 Reads are too small for use in assembly
244. Version highlights for GATK version 24
245. Release notes for GATK version 24
246. AGBT presentations are online
247. Release of 24 is delayed
248. The workshop videos Dec 2012 are online
249. Upcoming changes to the license amp the retirement of GATK Lite by v 24
250. What is most important for a QampA session
251. Consolidation of Ask the Team Ask the Community categories
252. Version highlights for GATK version 23
253. Release notes for GATK version 23
254. Presentation slides from Dec 45 2012 workshop
255. Upcoming documentation improvements and an appeal to Pay it forward
256. GATK workshop Dec 45 Register now
257. Job opening in the GATK dev team Broad req 916
258. Broken link reports
259. Release notes for GATK version 22
260. Version highlights for GATK version 22
261. Announcing details of the commercial licensing for GATK 2
262. GATK workshop Dec 45 Save the date
263. Slides from the Broad Institute Medical and Population Genetics Program meeting 9612
264. Notice Bug affecting ReduceReads GATK versions 20 and 21
265. Notice Bug affecting BQSR run with Queue scattergather
266. GATK variation discovery underlies deCODE Autism sequencing study 9394 confirmation rate
267. Release notes for GATK version 21
268. Announcing gsaannounce get an email whenever theres a new GATK release
269. Release notes for GATK version 20
270. GATK 20 announcement
Dictionary
Analysis submission status
Attribute
Authorization Domains
Bait bias
Biallelic vs Multiallelic sites
Biallelic vs Multiallelic sites
Bisulfite sequencing Cytosine methylation
Bisulfite sequencing Cytosine methylation
Call caching
CallTask submission status
Cluster
Coverage Read depth metrics
Cromwell
Data Library
Data Model
Docker container image registry
Docker container image registry
Downsampling
FASTA Reference genome format
Featured Workspace
FireCloud Billing Project
FireCloud Public API
Fishers Exact Test
Funcotator Annotation Specifications
GATK4 commandline syntax
GATKReport and gsalib
GenomicsDB
GitHub basics for researchers
Google Billing Account
Google bucket
Google Dataproc Spark cluster service
Google Pipelines API PAPI
GRCh37 hg19 b37 humanG1Kv37 Human Reference Discrepancies
Groups
GVCF Genomic Variant Call Format
Haplotype map format
Hardware optimizations SSD CPU GPU FPGA TPU
HDF5 format
Heterozygosity
Heterozygosity
Human genome reference builds GRCh38hg38 b37 hg19
Hybrid selection
Hybrid selection exome preparation
Inbreeding Coefficient
Intervals and interval lists
Intervals and interval lists
Jar caching
Jar caching and enabling it
JEXL filtering expressions
Jumping libraries
Jumping libraries
Known variants Training resources Truth sets
Lane Library Sample Cohort
Likelihoods and Probabilities
Likelihoods and Probabilities
Load files TSV files
Mate unmapped records
Mate unmapped records
Method
Method Access Controls
Method configuration
Method Repository
Monitor tab
OxoG oxidative artifacts
OxoG oxidative artifacts
Pair data model entity
Pairedend matepair
Pairedend matepair
Panel of Normals PON
Parallelism
Parallelism Multithreading Scatter Gather
Participant data model entity
PED Pedigree format
Pedigree PED files
PF reads Illumina chastity filter
PF reads Illumina chastity filter
Phredscaled Quality Scores
Phredscaled quality scores
Picard haplotype map file format
Preadapter artifacts in hybrid selection
Preadapter artifacts in hybrid selection Bait bias
Preemptibles
Proxy group
Rank Sum Test
Read filters
Read groups
Read groups
Reference genome
Reference Genome Components
RefSeq gene list format
Resource bundle
SAM BAM CRAM Mapped sequence data formats
Sample data model entity
Spanning or overlapping deletions allele
Spanning or overlapping deletions allele
Spark
Task
TCGA Controlled Access Data
TCGA Open Access Data
uBAM Unmapped BAM Format
Variant annotations
Variant annotations
VCF Variant Call Format
Version numbers
Workflow
Workflow Description Language WDL
Workflow submission status
Workspace
Workspace Access Controls
Workspace attributes
Workspace List
Workspace status
Frequently Asked Questions
Are there any Broadspecific instructions for using GATK
Are there any public Docker images to help me build my pipeline and tools for FireCloud
Are there Best Practices for calling variants in RNAseq data
At what point should I merge read group BAM files belonging to the same sample into a single file
Can I apply the germline variant joint calling workflow to my RNAseq data
Can I get a notification when my question is answered or commented on
Can I register for FireCloud with my current nonGmail email address
Can I use different versions of the GATK at different steps of my analysis
Can I use different versions of the GATK at different steps of my analysis
Can I use GATK on nondiploid organisms
Can runtime parameter values be generated dynamically
Collected FAQs about input files for sequence read data BAMCRAM
Collected FAQs about interval lists
Collected FAQs about VCF files
Do I need to create a Google Billing Account or FireCloud Billing Project to use FireCloud
Does GATK work on nondiploid organisms
Does it matter what browser I use with FireCloud
Does my data have to live in a Google bucket to be accessible to FireCloud
FAQs about the FireCloud Free Credits Program
How can I access datasets that were cataloged in the Library
How can I attendhost a GATK workshop
How can I invoke read filters and their arguments
How can I make GATK tools run faster
How can I prepare a FASTA file to use as reference
How can I run different versions of Java on the same computer
How can I stay up to date with FireCloud features and events
How can I turn on or customize forum notifications
How can I use parallelism to make GATK tools run faster
How do I submit a detailed bug report
How do I submit a detailed bug report
How does method versioning work
How much does it cost to use FireCloud
How should I cite GATK in my own publications
How should I cite GATK in my own publications
How should I prepare for a GATK workshop
How should I preprocess data from multiplexed sequencing and multilibrary designs
How should I preprocess data from multiplexed sequencing and multilibrary designs
How should I select samples for a Panel of Normals for somatic analysis
If I publish a Workspace in the Data Library who can see it
Im new to GATK Where do I start
Is FireCloud down
Lane library sample and cohort What do they mean and why are they important
Should I analyze my samples alone or together
Should I use UnifiedGenotyper or HaplotypeCaller to call variants on my data
What actions am I allowing when I register for FireCloud
What are quotas and how do I request more
What are the prerequisites for running GATK
What are the requirements for running GATK
What do GATK workshops cover
What do I need to do before attending a workshop handson session
What do I need to set up to write and execute WDL workflows
What do the VariantEval modules do
What input files does the GATK accept require
What input files does the GATK accept require
What is a GVCF and how is it different from a regular VCF
What is a VCF and how should I interpret it
What is GATKLite and how does it relate to full GATK 2x RETIRED
What is MapReduce and why are GATK tools called walkers
What is Phone Home and how does it affect me
What is the best way to get help with FireCloud
What is the difference between QUAL and GQ annotations
What is the GATKReport file format
What is the structure of a GATK command
What is the Terra Free Credits Program
What is uBAM and why is it better than FASTQ for storing unmapped sequence data
What should I use as known variantssites for running tool X
What types of variants can GATK tools detect handle
What types of variants can GATK tools detect handle
Whats in the resource bundle and how can I get it
When should I restrict my analysis to specific intervals
When should I use L to pass in a list of intervals
Where can I find known variants training and truth sets and other resource files
Where can I find the The Cancer Genome Atlas TCGA data in FC
Where can I get a gene list in RefSeq format
Where can I get help with WDL and Cromwell
Where can I get the GATK source code
Where can I get the GATK source code Is it opensource
Which tools use pedigree information
Which training sets arguments should I use for running VQSR
Which workflow execution engines support WDL What is Cromwell
Who can publish datasets in the Library
Why are some of the annotation values different with VariantAnnotator compared to UG or HC
Why cant I create or clone a workspace
Why is FireCloud requesting offline access
Why is my total run cost not available
GATK 4 Beta
ArrayIndexOutOfBoundsException error in BaseRecalibratorSpark
Creating a list of common SNPs for use with GetBayesianHetCoverage
Description and examples of the steps in the ACNV case workflow
Description and examples of the steps in the CNV case and CNV PoN creation workflows
GATK CNV Toolchain in Firehose and FAQ Broad Internal
GATK4 ApplyBQSRSpark VS PrintReadsSpark
GATK4Alpha MarkDuplicates crashing
How does the BwaSpark in GATK4 control the number of threads
How to Call somatic copy number variants using GATK4 CNV
How to Run FlagStatSpark on a cloud Spark cluster
How to Run the GATK4 Docker locally and take a look inside
HOWTO Run GATK CNV and GATK ACNV using premade Queue scripts Broad Internal
Howto Run GATK4 in a Docker container
Limits on the size of a PoN
No plots produced by AnalyzeCovariates GATK4Alpha
Overview of GetBayesianHetCoverage for heterozygous SNP calling
Segment Mean must be finite
Using GenomicsDBImport to consolidate GVCFs for input to GenotypeGVCFs in GATK4
WDL for GATK CNV and GATK ACNV
Which dotkits should you load to run GATK CNV or ACNV Broad Internal
Why is java using 1000 of my CPU when running a singlethreaded tool in gatkprotectedjar
GATK4 User Guide
GATK workshops
Getting started with GATK4
Methods and Algorithms
About Methods and Workflows
ActiveRegion determination HaplotypeCaller Mutect2
After gCNV calling considerations
Allelespecific annotation and filtering
Allelespecific annotation and filtering of germline short variants
Assigning persample genotypes HaplotypeCaller
Base Quality Score Recalibration BQSR
Base Quality Score Recalibration BQSR
Best Practices for Variant Discovery in DNAseq
Best Practices for Variant Discovery in RNAseq
Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs
Calling variants in RNAseq
Combining variants from different files into one
Difference between QUAL and GQ annotations in germline variant calling
Evaluating the evidence for haplotypes and variant alleles HaplotypeCaller Mutect2
Evaluating the quality of a germline short variant callset
Evaluating the quality of a variant callset
Genotype Refinement workflow
Genotype Refinement workflow for germline short variants
Genotype Refinement workflow mathematical details
HaplotypeCaller in a nutshell
HaplotypeCaller Reference Confidence Model GVCF mode
Hardfiltering germline short variants
HC overview How the HaplotypeCaller works
HC step 1 Defining ActiveRegions by measuring data entropy
HC step 2 Local reassembly and haplotype determination
HC step 3 Evaluating the evidence for haplotypes and variant alleles
HC step 4 Assigning persample genotypes
How the HaplotypeCallers reference confidence model works
Introduction to the GATK Best Practices workflows
Local Realignment around Indels
Local reassembly and haplotype determination HaplotypeCaller Mutect2
Math notes How PL is calculated in HaplotypeCaller
Math notes Understanding the QUAL score and its limitations
Performing sequence coverage analysis
Purpose and operation of Readbacked Phasing
Reference implementation PairedEndSingleSampleWf pipeline
Selecting variants of interest from a callset
Somatic calling is NOT simply a difference between two callsets
The logic of joint calling for germline short variants
Understanding and adapting the generic hardfiltering recommendations
Using depth of coverage metrics for variant evaluation
Using JEXL to apply hard filters or select variants based on annotation values
Variant Quality Score Recalibration VQSR
Variant Quality Score Recalibration VQSR
VariantEval Evaluation Modules Glossary
Quick Start Guide
FireCloud Terms of Service
Free Credits Program
Free Credits Program terms and conditions
Quick Start Part 1 Its all about the workspace
Quick Start Part 2 Workspace gt Summary
Quick Start Part 3 Workspace gt Data
Quick Start Part 4 Workspace gt Analysis
Quick Start Part 5 Workspace gt Notebooks
Quick Start Part 6 Workspace gt Method Configurations
Quick Start Part 7 Workspace gt Monitor
Solutions to Problems
Allele Depth AD is lower than expected
Allele Depth AD is lower than expected
AnalyzeCovariates fails with error message RScript exited with 1
Cant use VQSR on nonmodel organism or small dataset
Deep sequencing data is missing variants in M2 called vcf
Error message File is larger than 1000000 Bytes
Error messages Internal Server Error or Gateway Timeout
Errors about contigs in BAM or VCF files not being properly ordered or sorted
Errors about contigs in BAM or VCF files not being properly ordered or sorted
Errors about input files having missing or incompatible contigs
Errors about input files having missing or incompatible contigs
Errors about misencoded quality scores
Errors about misencoded quality scores
Errors about read group RG information
Errors about read group RG information
Errors in SAMBAM files can be diagnosed with ValidateSamFile
Errors in SAMBAM files can be diagnosed with ValidateSamFile
Exception in thread main javalangNoClassDefFoundError orgxerialsnappyLoadSnappy
Expected variant at a specific site was not called
I am unable to use VQSR recalibration to filter variants
I do not get the annotations I specified with A
I expect to see a variant at a specific site but its not getting called
I need to process readgrouplevel files but theres no obvious place for them in the data model
I need to run programs that require different versions of Java
Im getting an endless spinner Loading auth message when trying to access the web portal
Java is using too many resources threads memory or CPU
Java version issues
Known Issues with Mutect2 GATK41
Known Issues with VariantRecalibrator
Limitations of Notebooks Beta
Missing annotations in the output callset VCF
missing physical phasing information in vcf
My billing account isnt showing up or has an error message
Need to run programs that require different versions of Java
Placeholder please disregard
SelectVariants Cookbook
The program I want to run isnt available in a docker
VariantFiltration FT tag
Tutorials
(howto) Retrieve the time and cost of a completed workflow
1 howto Write your first WDL script running GATK HaplotypeCaller
2 howto Write a simple multistep workflow
3 howto Run a sample variant discovery minipipeline
4 howto Use scattergather to joint call genotypes
About Tutorials
Appendix to howto Discover variants with GATK
Get started with FireCloud
Guidelines for working with Docker Images and Dockerfiles Broadies only
How to Call somatic mutations using GATK4 Mutect2
How to Call somatic SNVs and indels using MuTect2
How to Consolidate GVCFs for joint calling with GenotypeGVCFs
How to Create a snippet of reads corresponding to a genomic interval
How to Execute Workflows from the gatkworkflows Git Organization
How to Filter on genotype using VariantFiltration
How to Filter variants either with VQSR or by hardfiltering
How to Fix a badly formatted BAM
How to Generate an unmapped BAM from FASTQ or aligned BAM
How to Install and use Conda for GATK4
How to Map and clean up short read sequence data efficiently
How to Map reads to a reference with alternate contigs like GRCh38
How to Mark duplicates with MarkDuplicates or MarkDuplicatesWithMateCigar
How to Simulate reads using a reference genome ALT contig
howto Access TCGA Controlled Access Data Workspaces
howto Add users to a FireCloud Billing Project
howto Apply hard filters to a call set
howto Call variants with HaplotypeCaller
howto Call variants with the UnifiedGenotyper
howto Cite FireCloud Cromwell or WDL in your publications
howto Configure a method in a workspace
howto Create a new FireCloud Billing Project
howto Create a new method
howto Create a workspace
howto Discover variants with GATK A GATK Workshop Tutorial
howto Evaluate a callset with CollectVariantCallingMetrics
howto Evaluate a callset with VariantEval
howto Generate a bamout file showing how HaplotypeCaller has remapped sequence reads
howto Generate a JSON file describing inputs
howto Get started with GATK4 beta
howto Import metadata
howto Install all software packages required to follow the GATK Best Practices
howto Install Docker and test that it works
howto Install software for GATK workshops
howto Install software for WDL workshops
howto Launch an analysis
howto Make a docker image the easy way using a base image
howto Overwrite and delete data from the data model
howto Perform local realignment around indels
howto Prepare for a FireCloud 101 workshop
howto Publish a docker container image to Google Container Registry GCR
howto Recalibrate base quality scores run BQSR
howto Recalibrate variant quality scores run VQSR
howto Register get an account to use FireCloud
howto Revert a BAM file to FastQ format
howto Run a WDL script via Cromwell on a local machine eg your laptop
howto Run Queue for the first time
howto Run the GATK for the first time
howto Run the genotype refinement workflow
howto Run workflows on sets
howto Set up a Google Billing Account Broadies only
howto Set up a Google Billing Account nonBroad users
howto Set up an environment to test your workflows locally
howto Set up billing
howto Set up use and shut down a Notebook
howto Test your GATK installation
howto Test your Queue installation
howto Upload files to your Google bucket
howto Use my own tools in FireCloud
howto Validate your WDL script syntax before execution
howto Visualize an alignment with IGV
Troubleshooting in FireCloud
Tutorial files provenance ASHG15
GATK4 User Guide
This section contains the GATK4 documentation. This content is best viewed at
https://software.broadinstitute.org/gatk/userguide
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click
here
GATK workshops
Getting started with GATK4
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