GenomicsDBImport

Discussion List

• GATK 4.1.1.0 GenomicsDBImport error : Duplicate fields exist in vid attribute "fields" and 2 errors

  Answered 25 views 4 comments 0 points Most recent by Wonton July 16Ask the GATK team
• GATK 4.1.1.0 GenomicsDBImport error : Duplicate field name AF found in vid attribute "fields"

  Accepted Answer 208 views 6 comments 0 points Most recent by Rishabh July 12Ask the GATK team
• GenomicsDBImport run slowly with multiple samples

  Accepted Answer 741 views 26 comments 1 point Most recent by evetc July 8Ask the GATK team
• GenomicsDBImport or CombineGvcfs on WGS dataset

  Accepted Answer 49 views 3 comments 0 points Most recent by bhanuGandham June 27Ask the GATK team
• GenomicsDBImport too slow on local server

  Accepted Answer 285 views 6 comments 0 points Most recent by Alexandra June 24Ask the GATK team
• --intervals input in GenomicsDBImport for non model de novo genome

  Answered 81 views 3 comments 0 points Most recent by bhanuGandham June 18Ask the GATK team
• Error with GenomicsDBImport input file

  Accepted Answer 26 views 1 comment 0 points Most recent by nparmalee June 6Ask the GATK team
• PON: Mutect2 include MNPs and crash GenomicsDBImport

  Accepted Answer 236 views 12 comments 0 points Most recent by bhanuGandham May 24Ask the GATK team
• GenomicsDBImport 4.1.2.0 on very large WES cohort : java.lang.OutOfMemoryError

  Accepted Answer 46 views 4 comments 0 points Most recent by emixaM May 10Ask the GATK team
• How to combine the interval after GenomicsDBImport

  Answered 113 views 5 comments 1 point Most recent by vang May 3Ask the GATK team
• Invalid gzip header in genomicsdbimport

  Accepted Answer 41 views 2 comments 0 points Most recent by bhanuGandham April 24Ask the GATK team
• Potential for merging GenomeDBs or adding to an existing database

  Answered 26 views 1 comment 0 points Most recent by bhanuGandham April 16Ask the GATK team
• GenomicsDBImport haploid data ?

  Answered 78 views 5 comments 0 points Most recent by slament April 11Ask the GATK team
• genomicsDBimport --merge-input-intervals explanation

  Answered 102 views 1 comment 0 points Most recent by bhanuGandham April 9Ask the GATK team
• (How to) Consolidate GVCFs for joint calling with GenotypeGVCFs

  2.7K views 25 comments 0 points Most recent by danat_yermakovich April 9Tutorials
• Workflow for GenomicsDBImport and GenotypeGVCFs across multiple intervals

  Answered 88 views 2 comments 0 points Most recent by mpj5142 April 1Ask the GATK team
• Can i skip GenomicsDBimport and CombinedGVCFs?

  Accepted Answer 45 views 3 comments 0 points Most recent by bshifaw March 21Ask the GATK team
• Running GenomicsDBImport: stuck on 'INFO GenomicsDBImport - Importing batch 1 with 62 samples'

  Answered 28 views 1 comment 0 points Most recent by bhanuGandham March 18Ask the GATK team
• GenomicsDBImport file opening error

  Accepted Answer 44 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 40 views 1 comment 0 points Most recent by SChaluvadi February 12Ask the GATK team
• How to consolidate 81 GVCF files for 35,000 intervals ?

  Answered 46 views 1 comment 0 points Most recent by bshifaw January 23Ask the GATK team
• GATK v4.0.8.1 GenomicsDBImport Error (VariantStorageManagerException exception)

  Answered 298 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 725 views 11 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• GenomicsDBImport--do multiple samples need individual databases?

  Answered 279 views 8 comments 0 points Most recent by yingchen69 November 2018Ask the GATK team
• GenomicsDBImport - Duplicate field name MQ0 found in vid map

  Answered 155 views 7 comments 0 points Most recent by lelimat November 2018Ask the GATK team
• GenomicsDBImport error

  Accepted Answer 171 views 16 comments 0 points Most recent by biojiangke November 2018Ask the GATK team
• GenomicsDBImport "RunConfigException" Error when scale is high

  Accepted Answer 113 views 12 comments 0 points Most recent by Kousik November 2018Ask the GATK team
• GenomicsDBImport bus error

  Accepted Answer 94 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 368 views 5 comments 0 points Most recent by bhanuGandham October 2018Ask the GATK team
• GenomicsDBImport

  Accepted Answer 146 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 229 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 66 views 2 comments 0 points Most recent by adam_s October 2018Ask the GATK team
• Failure while waiting for FeatureReader to initialize ?

  Answered 90 views 1 comment 0 points Most recent by bshifaw October 2018Ask the GATK team
• Unsure if GenomicsDBImport worked properly

  Answered 56 views 1 comment 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• GenomicsDBImport creating lots of "temporary" files

  Answered 42 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 171 views 1 comment 0 points Most recent by Yatros September 2018Ask the Cromwell + WDL Team
• Difference in GenotypeGVCFs generated VCF after consolidation with GenomicsDBimport and CombineGVCF

  Answered 99 views 5 comments 0 points Most recent by Sheila June 2018Ask the GATK team
• GATK4beta6 annotation incompatibility between HaplotypeCaller and GenomicsDBImport

  Answered 265 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 79 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 217 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 430 views 2 comments 0 points Most recent by nrockweiler March 2018Ask the Cromwell + WDL Team
• GATK not found when running WDL script locally

  Accepted Answer 272 views 2 comments 0 points Most recent by ChrisL February 2018Ask the Cromwell + WDL Team
• Problem parsing interval list file to GenomicsDBImport

  Accepted Answer 764 views 7 comments 0 points Most recent by Yatros February 2018Ask the GATK team
• GenomicsDBimport multijob issue

  Answered 80 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2017Ask the GATK team
• Problem using GATK4 GenomicsDBImport for joint calling.

  Accepted Answer 463 views 3 comments 0 points Most recent by Sheila December 2017Ask the GATK team