GenomicsDBImport

Discussion List

• GenomicsDBImport file opening error

  Accepted Answer 27 views 2 comments 0 points Most recent by danangcrysnanto February 16Ask the GATK team
• Filter coding germline variants from 100 human WGS gVCFs

  Accepted Answer 18 views 1 comment 0 points Most recent by SChaluvadi February 12Ask the GATK team
• (How to) Consolidate GVCFs for joint calling with GenotypeGVCFs

  1.6K views 19 comments 0 points Most recent by danangcrysnanto February 7Tutorials
• How to consolidate 81 GVCF files for 35,000 intervals ?

  Answered 35 views 1 comment 0 points Most recent by bshifaw January 23Ask the GATK team
• GATK v4.0.8.1 GenomicsDBImport Error (VariantStorageManagerException exception)

  Answered 178 views 6 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• Are there any plans to add multi-interval support to GenomicsDBImport?

  Accepted Answer 575 views 11 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• GenomicsDBImport--do multiple samples need individual databases?

  Answered 172 views 8 comments 0 points Most recent by yingchen69 November 2018Ask the GATK team
• GenomicsDBImport - Duplicate field name MQ0 found in vid map

  Answered 110 views 7 comments 0 points Most recent by lelimat November 2018Ask the GATK team
• GenomicsDBImport error

  Accepted Answer 133 views 16 comments 0 points Most recent by biojiangke November 2018Ask the GATK team
• GenomicsDBImport "RunConfigException" Error when scale is high

  Accepted Answer 91 views 12 comments 0 points Most recent by Kousik November 2018Ask the GATK team
• GenomicsDBImport bus error

  Accepted Answer 61 views 5 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• GATK4 joint Genotyping for an exome pipeline: CombineGVCFs or GenomicsDBImport ?

  Answered 242 views 5 comments 0 points Most recent by bhanuGandham October 2018Ask the GATK team
• GenomicsDBImport

  Accepted Answer 99 views 4 comments 0 points Most recent by HectorMarina October 2018Ask the GATK team
• Trouble getting combined gvcf file using either GenomicsDBImport or CombineGVCFs

  Accepted Answer 144 views 3 comments 0 points Most recent by QuinnC October 2018Ask the GATK team
• Very long import time heavily compounded across a transcriptome in GenomicsDBImport

  Answered 58 views 2 comments 0 points Most recent by adam_s October 2018Ask the GATK team
• Failure while waiting for FeatureReader to initialize ?

  Answered 56 views 1 comment 0 points Most recent by bshifaw October 2018Ask the GATK team
• Unsure if GenomicsDBImport worked properly

  Answered 51 views 1 comment 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• GenomicsDBImport creating lots of "temporary" files

  Answered 32 views 1 comment 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• GenomicsDBimport failed to create reader error with updated joint-discovery-gatk4-local.wdl pipeline

  Accepted Answer 80 views 1 comment 0 points Most recent by Yatros September 2018Ask the Cromwell + WDL Team
• GenomicsDBImport run slowly with multiple samples

  Accepted Answer 312 views 15 comments 1 point Most recent by TonyWei July 2018Ask the GATK team
• Difference in GenotypeGVCFs generated VCF after consolidation with GenomicsDBimport and CombineGVCF

  Answered 58 views 5 comments 0 points Most recent by Sheila June 2018Ask the GATK team
• GenomicsDBImport haploid data ?

  Answered 44 views 2 comments 0 points Most recent by Sheila May 2018Ask the GATK team
• GATK4beta6 annotation incompatibility between HaplotypeCaller and GenomicsDBImport

  Answered 224 views 34 comments 0 points Most recent by shlee April 2018Ask the GATK team
• GenomicsDBImport problem with versions 0.9.0 and 0.9.2

  Accepted Answer 60 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• Workaround for the GenomicsDBImport + Draft Assemblies + Firecloud = World of Pain Equation

  Accepted Answer 187 views 8 comments 0 points Most recent by jasongallant1 March 2018Ask the FireCloud Team
• Accessing local files in host machine while running WDL/CROMWELL script / Mount volume automatically

  Accepted Answer 313 views 2 comments 0 points Most recent by nrockweiler March 2018Ask the Cromwell + WDL Team
• GenomicsDBImport too slow on local server

  Accepted Answer 210 views 3 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• GATK not found when running WDL script locally

  Accepted Answer 194 views 2 comments 0 points Most recent by ChrisL February 2018Ask the Cromwell + WDL Team
• Problem parsing interval list file to GenomicsDBImport

  Accepted Answer 605 views 7 comments 0 points Most recent by Yatros February 2018Ask the GATK team
• GenomicsDBimport multijob issue

  Answered 68 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2017Ask the GATK team
• Problem using GATK4 GenomicsDBImport for joint calling.

  Accepted Answer 400 views 3 comments 0 points Most recent by Sheila December 2017Ask the GATK team