adam2vcf doesn't have info fields #939

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andrewmchen commented Feb 12, 2016

I added info fields only if the vcf is from a single sample.

What's the desired behavior if the vcf has multiple samples per site?

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GitHub pull request #939 of commit f3b09ed automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/939/merge^{commit} # timeout=10 > git branch -a --contains 68e0faef576be5033a341ce95b2e47757c630a07 # timeout=10 > git rev-parse remotes/origin/pr/939/merge^{commit} # timeout=10Checking out Revision 68e0faef576be5033a341ce95b2e47757c630a07 (origin/pr/939/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 68e0faef576be5033a341ce95b2e47757c630a07First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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Build result: FAILURE

GitHub pull request #939 of commit f3b09ed automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/939/merge^{commit} # timeout=10 > git branch -a --contains 68e0faef576be5033a341ce95b2e47757c630a07 # timeout=10 > git rev-parse remotes/origin/pr/939/merge^{commit} # timeout=10Checking out Revision 68e0faef576be5033a341ce95b2e47757c630a07 (origin/pr/939/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 68e0faef576be5033a341ce95b2e47757c630a07First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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Whoops! You should have an info field per site, as well as sample specific annotations (per sample, per site), see https://samtools.github.io/hts-specs/VCFv4.2.pdf. Essentially, the info field behavior should be the same in the single and multi sample cases.

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fnothaft commented Feb 12, 2016

Whoops! You should have an info field per site, as well as sample specific annotations (per sample, per site), see https://samtools.github.io/hts-specs/VCFv4.2.pdf. Essentially, the info field behavior should be the same in the single and multi sample cases.

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Hm I read through the VCF spec and I don't think I completely understand still.

First, my understanding was that before this PR we wouldn't have any per site info field. Second, when convert a VCF to a RDD of adam Genotypes, are the VariantCallingAnnotations statistics not per sample but instead statistics aggregated across samples from that site?

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andrewmchen commented Feb 16, 2016

Hm I read through the VCF spec and I don't think I completely understand still.

First, my understanding was that before this PR we wouldn't have any per site info field. Second, when convert a VCF to a RDD of adam Genotypes, are the VariantCallingAnnotations statistics not per sample but instead statistics aggregated across samples from that site?

@heuermh heuermh added this to the 0.20.0 milestone Feb 22, 2016

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heuermh Feb 22, 2016

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@andrewmchen after we get 0.19.0 out, I plan to focus on VCF INFO handling, for supporting the VCF ANN spec and other related issues. Please let me know how I might help in a week or so.

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heuermh commented Feb 22, 2016

@andrewmchen after we get 0.19.0 out, I plan to focus on VCF INFO handling, for supporting the VCF ANN spec and other related issues. Please let me know how I might help in a week or so.

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@heuermh Sure! Would love to work with you on some of the VCF features. Right now I'm just playing around with it for the purposes of avocado.

Maybe this isn't the desired behavior, but I think it's kind of strange that adam2vcf returns a much different vcf than the original that was passed into vcf2adam. Are the related issues you mentioned related to this?

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andrewmchen commented Feb 22, 2016

@heuermh Sure! Would love to work with you on some of the VCF features. Right now I'm just playing around with it for the purposes of avocado.

Maybe this isn't the desired behavior, but I think it's kind of strange that adam2vcf returns a much different vcf than the original that was passed into vcf2adam. Are the related issues you mentioned related to this?

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fnothaft May 18, 2016

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I will open a follow on PR that addresses some issues with this (specifically, stores sample info in genotype, aggregate in INFO).

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fnothaft commented May 18, 2016

I will open a follow on PR that addresses some issues with this (specifically, stores sample info in genotype, aggregate in INFO).

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@heuermh is this good to go on your side? I just looked in more detail and think it is fine (doesn't need any more patches). If it is good from your side, then I will merge.

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fnothaft commented May 20, 2016

@heuermh is this good to go on your side? I just looked in more detail and think it is fine (doesn't need any more patches). If it is good from your side, then I will merge.

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LGTM

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heuermh commented May 20, 2016

LGTM

@fnothaft fnothaft merged commit 22259c1 into bigdatagenomics:master May 21, 2016

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fnothaft May 21, 2016

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Merged! Thanks @andrewmchen!

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fnothaft commented May 21, 2016

Merged! Thanks @andrewmchen!

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