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Jannovar error thrown when annotating VCFs #341

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meatcar opened this issue Jul 14, 2014 · 0 comments
Closed

Jannovar error thrown when annotating VCFs #341

meatcar opened this issue Jul 14, 2014 · 0 comments

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@meatcar
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meatcar commented Jul 14, 2014

This is an issue that is not present in #335, but is present in the current master, and hence the 1.3 build.

When importing a VCF, in the annotation stage an exception is thrown on https://github.com/compbio-UofT/medsavant/blob/master/jannovar/src/main/java/jannovar/Jannovar.java#L929

The right way to fix this would be to pass the genome version to Jannovar when annotating. However, I am unsure what should be done if a project uses both hg18 and hg19, i.e. when both checkboxes are checked on creation.

meatcar added a commit that referenced this issue Jul 14, 2014
I forgot to add genome reference passing when initializing Jannovar.
This should make the 1.3.1 build actually testable.
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