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TRASA • 0
@trasa-17881
Last seen 3.3 years ago

Hi

I am trying to convert Vcf files to VRanges objects. However, I get following Error message

readVcfAsVRanges(vcf1)
Error in validObject(.Object) :   invalid class "VRanges" object: 'refDepth' must be non-negative


I found this support post: https://stat.ethz.ch/pipermail/bioconductor/2014-June/060121.html. According to this I confirmed that I really have negative AD values in my vcf file. Following the instruction in the post I can circumvent this to still generate VRanges files. However, I am not completely sure what this negative AD value means and whether this is a problem. Can somebody help me with that? Under which condition can a negative AD value be generated?

Thanks.

VariantAnnotation • 386 views
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@michael-lawrence-3846
Last seen 10 months ago
United States

Best to ask the maintainer of whatever generated the VCF file.