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Support VCF annotation ANN field in vcf2adam and adam2vcf #1044

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heuermh opened this issue Jun 5, 2016 · 5 comments
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Support VCF annotation ANN field in vcf2adam and adam2vcf #1044

heuermh opened this issue Jun 5, 2016 · 5 comments
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@heuermh
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@heuermh heuermh commented Jun 5, 2016

Schema were added to bdg-formats in bigdatagenomics/bdg-formats#67.

@fnothaft
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@fnothaft fnothaft commented Nov 8, 2016

Should be resolved by #1250.

@heuermh
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@heuermh heuermh commented Nov 11, 2016

#1250 doesn't fully address this yet.

Mappings between the VCF INFO reserved key ANN and calls to TranscriptEffectConverter.convertToTranscriptEffects and TranscriptEffectConverter.convertToVcfInfoAnnValue need to be added to VariantAnnotationConverter as part of further refactoring.

@jpdna
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@jpdna jpdna commented Nov 16, 2016

#1271 should address this correct?

@heuermh
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@heuermh heuermh commented Nov 16, 2016

No, I haven't written the code yet. :)

Look for a new pull request that says it fixes this issue.

@heuermh
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@heuermh heuermh commented Jan 5, 2017

Fixed by #1288

@heuermh heuermh closed this Jan 5, 2017
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