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Add multi-interval support to GenomicsDBImport #3269

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droazen opened this issue Jul 13, 2017 · 6 comments
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Add multi-interval support to GenomicsDBImport #3269

droazen opened this issue Jul 13, 2017 · 6 comments
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@kgururaj
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enhancement GenomicsDB
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Engine-2Q2018

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@droazen
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droazen commented Jul 13, 2017

GenomicsDBImport is currently designed for scattering on a cluster, and so accepts only a single interval per invocation. To make it easier to run the tool locally as a replacement for CombineGVCFs, we should add the ability to pass in multiple intervals at once.
@droazen
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droazen commented Jul 13, 2017

For @kgururaj and @kdatta

@droazen droazen added this to the Engine-4.0 milestone Jul 13, 2017
@droazen droazen modified the milestones: Engine-4.0, Engine-4.1 Oct 17, 2017
@droazen droazen mentioned this issue Jan 18, 2018
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@ptranvan
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ptranvan commented Mar 7, 2018

Multi intervals working now ?

@droazen
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droazen commented Mar 7, 2018

Not yet @ptranvan. @kgururaj and his team have a patch coming soon to add multi-interval support to this tool, so there's a good chance it will make it into a GATK release this month.

@vdauwera vdauwera mentioned this issue Mar 8, 2018
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@francares francares mentioned this issue May 4, 2018
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@ajshultz
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Hello,
Any update to the timeline here? It looks like there is only some lasts tests to be run? I am eagerly awaiting multi-interval support for a project I am working on. Thank you for all of your hard work!

@droazen
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droazen commented Jun 20, 2018

Should not be much longer @ajshultz -- #4645 just needs a final review pass, so it's likely to make the next GATK release.

@droazen
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droazen commented Jul 6, 2018

Implemented in #4645

@droazen droazen closed this as completed Jul 6, 2018
@shalabhsuman shalabhsuman mentioned this issue Nov 7, 2018
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enhancement GenomicsDB
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@droazen @ajshultz @kgururaj @ptranvan