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Integrate Picard and GATK report formats #251

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yfarjoun opened this issue Mar 4, 2015 · 3 comments
Closed

Integrate Picard and GATK report formats #251

yfarjoun opened this issue Mar 4, 2015 · 3 comments
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enhancement PRIORITY_LOW QuixoticDream

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@yfarjoun
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yfarjoun commented Mar 4, 2015

Picard and GATK have different (incompatible) mechanisms for report generation.

I woudl strongly advocate finding out what the requirements are and merging the two systems.
@akiezun
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akiezun commented Apr 15, 2015

@yfarjoun what are the requirements?

@yfarjoun
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  • human/java/R readable
  • for picard, need to beable to repopulate metrics class from file
  • for gatk need to be able to read into r list of dataframes
  • javadoc generation of metrics description from comments in class (as in
    picard)
  • for picard: need to allow one table and one histogram
  • for GATK need to allow multiple different tables

On Wed, Apr 15, 2015 at 12:42 PM, Adam Kiezun [email protected]
wrote:

@yfarjoun https://github.com/yfarjoun what are the requirements?

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Reply to this email directly or view it on GitHub
#251 (comment)
.

@akiezun akiezun changed the title Reports! Integrate Picard and GATK report formats Apr 19, 2015
@droazen
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droazen commented Mar 22, 2017

Not happening -- closing

@droazen droazen closed this as completed Mar 22, 2017
schaluva added a commit that referenced this issue Mar 18, 2021
@schaluva
#251 Address gvcf no-calls missing QUALapprox and other features (#7146)
79d1a47 
* write variants with GQ no call to PET as GQ 0 and omit from VET

* remove unused imports

* update integration test with no_calls vcf file and ingest files

* created constant for sample index and modified comments

* create static method for isNoCall

* remove static import of method
mmorgantaylor pushed a commit that referenced this issue Apr 6, 2021
@schaluva @mmorgantaylor
#251 Address gvcf no-calls missing QUALapprox and other features (#7146)
072a4ae 
* write variants with GQ no call to PET as GQ 0 and omit from VET

* remove unused imports

* update integration test with no_calls vcf file and ingest files

* created constant for sample index and modified comments

* create static method for isNoCall

* remove static import of method
This was referenced Mar 17, 2023
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enhancement PRIORITY_LOW QuixoticDream
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@droazen @akiezun @yfarjoun