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Error with metadata: Multivalued flags are not supported for INFO lines #1669
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?
@dmmiller612 I don't believe multivalued flags are supported by the VCF specification. There is a
Number=A is cardinality; it means there is one value for each [A]llele.
There is some discussion about the specification issue here
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