Blogs
~ From Newest to Oldest ~
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
From newest to oldest
001. Catching up with the times GATK is moving to a new web home
002. GATK WDL Cromwell and Terra at ASHG 2019
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
029. New year new Comms team members
030. CrossSpecies Contamination Identification with PathSeq
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
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
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
056. Service note forum on break support resumes Nov 27
057. IMPORTANT Bug alert for GATK4 GenomicsDBImport
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
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
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
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
118. GATK Workshops World Tour 2016
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
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
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
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
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
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
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
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