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Error with metadata: Multivalued flags are not supported for INFO lines #1669

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dmmiller612 opened this issue Aug 17, 2017 · 4 comments
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@dmmiller612
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@dmmiller612 dmmiller612 commented Aug 17, 2017

Hello,

I have ran into an issue with one of the headers in my vcf file, where Adam throws the error: Multivalued flags are not supported for INFO lines: INFO=<ID=SNP,Number=A,Type=Flag,Description="Variant is a SNP">

I saw in VariantContextConverter on line 1272 where the error was getting thrown. Do multivalued flags cause problems? Is there any type of work around this issue? Can we skip the INFO metadata somehow when loading a variant rdd?

@heuermh
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@heuermh heuermh commented Aug 17, 2017

@dmmiller612 I don't believe multivalued flags are supported by the VCF specification. There is a ValidationStringency parameter that you can use, try setting it to ValidationStringency.LENIENT, although I don't know if that allows processing to continue after this kind of error.

@dmmiller612
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@dmmiller612 dmmiller612 commented Aug 17, 2017

Interesting. This annotation came from SnpSift, so I figured it was okay. I can't find exactly what is multivalued about that flag. It just says that the number is alphanumeric, is that the problem?

@heuermh
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@heuermh heuermh commented Aug 17, 2017

Number=A is cardinality; it means there is one value for each [A]llele.

There is some discussion about the specification issue here
samtools/hts-specs#123 (comment)

There is some draft doc on our VCF to bdg-formats mapping here, although it still needs cleanup and to find a home somewhere in ADAM docs
https://github.com/heuermh/bdg-formats/blob/docs/docs/source/variants.md

@heuermh heuermh modified the milestone: 0.23.0 Sep 1, 2017
@fnothaft fnothaft removed this from the 0.23.0 milestone Sep 12, 2017
@fnothaft fnothaft added the wontfix label Sep 12, 2017
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@fnothaft fnothaft commented Sep 12, 2017

Per discussion between me and @heuermh, this VCF is out of compliance with the spec, and we are not able to patch this issue in ADAM. We'll close this as a won't fix. You should be able to work around this with validation stringency.

@fnothaft fnothaft closed this Sep 12, 2017
@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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