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enable --includeNonVariantSites GenotypeGVCFS option #2865

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droazen opened this issue Jun 5, 2017 · 15 comments

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@droazen
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commented Jun 5, 2017

@lbergelson commented on Tue Jun 21 2016

Update genotype gvcfs so includeNonVariantSites can be enabled. This may be easiest by implementing a different walker type to match the old LocusWalker behavoir but could also be done by accumulating sites as it goes.


@lbergelson commented on Fri Apr 07 2017

this is blocked by #2429

@droazen droazen added this to the engine-4.0 milestone Jun 5, 2017

@droazen droazen changed the title enable --includeNonVariantSites GenotypeGVCS option enable --includeNonVariantSites GenotypeGVCFS option Oct 17, 2017

@droazen droazen removed this from the Engine-4.0 milestone Oct 17, 2017

@droazen droazen added this to the Engine-4.1 milestone Feb 5, 2018

@chandrans

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commented Mar 28, 2018

We have at least 5 users who are excited for this to go in.

@jleinenbach

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commented Apr 7, 2018

Whatshap needs this option.

@melisakman

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commented May 2, 2018

It would be great to have this option. +1 here!

@nealplatt

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commented May 4, 2018

I'd love to see this option implemented.

@citscisean

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commented May 21, 2018

I would love to see this as well.

@jiyongkun

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commented Jul 6, 2018

I need this option as well!

@danilovkiri

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commented Jul 23, 2018

Me too!

@jjfarrell

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commented Aug 3, 2018

I also need this option.

@marchoeppner

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commented Aug 15, 2018

Same...

@janrehker

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commented Aug 22, 2018

This feature would help me obliterate a horrible, horrible hack in my pipeline, thus replacing it with a solution of delight and beauty.
+1

@droazen

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commented Aug 22, 2018

We plan to assign someone to implement this feature within the next 1-2 months, so you shouldn't have to wait much longer for it.

@droazen

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commented Sep 4, 2018

May be able to use the existing MultiVariantWalkerGroupedOnStart traversal

@droazen droazen assigned cmnbroad and unassigned lbergelson Sep 4, 2018

@droazen

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commented Sep 4, 2018

Re-assigning to @cmnbroad

@13am

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commented Sep 12, 2018

+1

@sooheelee sooheelee reopened this Feb 1, 2019

@sooheelee

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commented Feb 1, 2019

Opened to connect to the relevant PR at #5219.

@sooheelee sooheelee closed this Feb 1, 2019

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