gatk3

Discussion List

• How can I debug and develop the algorithm in GATK ,such as haplotypecaller, use Intellij IDEA?

  Answered 40 views 1 comment 0 points Most recent by bhanuGandham December 2019Ask the GATK team
• Can we do variation analysis if we do not have vcf file hat genome

  Answered 18 views 2 comments 0 points Most recent by bhanuGandham June 2019Ask the GATK team
• Introduction to the GATK Best Practices workflows

  10.1K views 4 comments 0 points Most recent by KKND May 2019Methods and Algorithms
• Difference between dbsnp file in gatk3 and germline-resource file in gatk4 in Mutect2 analysis?

  Answered 110 views 1 comment 0 points Most recent by bhanuGandham May 2019Ask the GATK team
• Difference between HC and UG methods

  Answered 86 views 1 comment 0 points Most recent by bhanuGandham March 2019Ask the GATK team
• Rounds of BQSR in GATK3 GenericPreProcessingWorkflow

  Accepted Answer 59 views 4 comments 0 points Most recent by AdelaideR January 2019Ask the GATK team
• Generating a vcf with the information of specific genome positions (hotspots)

  Answered 141 views 3 comments 0 points Most recent by SChaluvadi December 2018Ask the GATK team
• Add GATK3 Variant Refinement

  Accepted Answer 54 views 5 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• GATK4 vs GATK3 output file compatability

  Accepted Answer 117 views 2 comments 0 points Most recent by map2085 July 2018Ask the GATK team
• i am running haplotypcaller in one bam file

  Answered 304 views 1 comment 0 points Most recent by Sheila June 2018Ask the GATK team
• GATK4 Realign around indels

  Answered 234 views 1 comment 0 points Most recent by Sheila February 2018Ask the GATK team
• CombineVariants Key . found in VariantContext field INFO but this key isn't defined in the VCFHeader

  Answered 554 views 3 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• Mutect2 outputting samples with AD of "."

  Answered 42 views 3 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• Testing Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)

  Answered 482 views 3 comments 0 points Most recent by agosto February 2018Ask the GATK team
• Release notes for GATK version 3.8

  493 views 0 comments 0 points Started by Geraldine_VdAuwera July 2017 Announcements
• Anticipate "--fix_misencoded_quality_scores"

  Accepted Answer 205 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017Ask the GATK team
• gatk haplotypecaller for gvcf

  Answered 236 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2016Ask the GATK team
• Release notes for GATK version 3.7

  701 views 0 comments 0 points Started by Geraldine_VdAuwera December 2016 Announcements
• Release notes for GATK version 3.6

  2K views 3 comments 0 points Most recent by Geraldine_VdAuwera June 2016Announcements
• Release notes for GATK version 3.5

  1.6K views 7 comments 0 points Most recent by Geraldine_VdAuwera February 2016Announcements
• Release notes for GATK version 3.4

  2.5K views 27 comments 0 points Most recent by Sheila September 2015Announcements
• Release notes for GATK version 3.3

  1.8K views 2 comments 0 points Most recent by Geraldine_VdAuwera February 2015Announcements
• Workflow for fungal WGS

  891 views 3 comments 0 points Most recent by simono101 January 2015Ask the GATK team
• GATK3 ApplyRecalibration doesn't work

  Answered 473 views 2 comments 0 points Most recent by shazly October 2014Ask the GATK team
• GenotypeGVCFs

  Answered 320 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2014Ask the GATK team
• Minor license text updates for GATK 3.x

  284 views 2 comments 0 points Most recent by Geraldine_VdAuwera September 2014Announcements
• Question about CombineGVCFs results

  Accepted Answer 416 views 6 comments 0 points Most recent by srynearson1 June 2014Ask the GATK team
• GATK 3.0+ LOD issue with VariantRecalibrator Running Large data sets .

  Accepted Answer 382 views 4 comments 0 points Most recent by srynearson1 May 2014Ask the GATK team
• Slides from the 4/10 webinar on GATK 3 features

  309 views 2 comments 0 points Most recent by Geraldine_VdAuwera May 2014Announcements
• Special webinar on GATK 3 features (4/10)

  266 views 0 comments 0 points Started by Geraldine_VdAuwera April 2014 Announcements
• GATK3.0 walker log output goes to stderr instead of stdout

  Accepted Answer 312 views 1 comment 0 points Most recent by pdexheimer March 2014Ask the GATK team