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port CombineVariants #17

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akiezun opened this issue Dec 10, 2014 · 7 comments

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@akiezun
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commented Dec 10, 2014

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@akiezun akiezun added the tools label Dec 11, 2014

@akiezun akiezun changed the title CombineVariants as a CLP port CombineVariants Feb 27, 2015

@akiezun akiezun added this to the Coelacanth milestone Feb 27, 2015

@akiezun akiezun removed this from the Coelacanth milestone Apr 15, 2015

@akiezun

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commented Apr 20, 2015

the requirement is to port the CombineVariants tool and tests. Current tests use Broad-visible data and that data needs to be reviewed and shared publicly if possible.

@akiezun akiezun modified the milestone: beta Jul 22, 2015

@droazen droazen removed this from the beta milestone Mar 28, 2016

lbergelson pushed a commit that referenced this issue May 31, 2017
Added tool to create the Panel of Normals:
  - CreatePanelOfNormals

Addresses issues #18 #17 #16 #15 and #7.

Test code for the new feature. Please squash before merging.

Added R script use to generete in input Pcovs for testing

Fixed some issues arising from merge.

Updated input test files to match what comes from ExomeReadCounts.
@davidbenjamin

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commented Jun 14, 2018

@lbergelson Can we close this issue since we now use MergeVcfs in the picard package? 3 1/2 years is a long time to be high priority. . .

@bhanugandham

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commented Oct 15, 2018

Users have shown interest in porting CombineVariants to GATK4. Features such as, combining vcfs with variants present in all or a fraction of samples exists in CombineVariants but not in MergeVcfs/SelectVariants. It would be helpful to look into this.

@ldgauthier

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commented Oct 16, 2018

The behavior of the GATK3 CombineVariants was very inconsistent and the arguments weren't entirely clear. I also suspect that some operations weren't possible with the arguments given. Rather than port that old broken version, I would advocate for an overhaul or rewrite.

@bhanugandham it's going to be a big project to collect requirements and expected behavior for this tool. For example, what should the MQ be for the combined VCF for two different input VCFs with different MQ values? Much of the confusion stemmed from the old ability to merge VCFs containing the same sample. In the case where we take one genotype for each sample name (e.g. the old -genotypeMergeOptions PRIORITIZE) then I believe the old behavior was wrong in some cases, taking the filter status from an input VCF at random. We also need to clarify FilteredRecordMergeType options, e.g. broadinstitute/gsa-unstable#935

@droazen

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commented Oct 16, 2018

I wonder if users mainly just want something that adds the "set" annotation, so that you can do things like -select 'set == "Intersection"' in SelectVariants...

@bhanugandham

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commented Oct 18, 2018

@ldgauthier what do you suggest the course of action should be? I mean for when users ask for certain feature that were in CombineVariants but not in MergeVcfs? Should I just create a new issue for each argument request?

@bhanugandham

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commented Oct 18, 2018

I have asked the users who requested porting CombineVariants for specific features that do not exist in MergeVcfs or other tools in gatk4, and are useful to them.
I will post results from that here, that should help make a decision.

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