locateVariants returns an empty result
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Entering edit mode
3.4 years ago
boris • 0

Hi! I'm having trouble using VariantAnnotation. When I try to assign variants (be it somatic variants or indels) to genes I get the following error:

all <- locateVariants(common[[1]], txdb, AllVariants())
Warning message:
In .returnEmpty() : none of seqlevels(query) match seqlevels(subject)

What does this error mean? I have about 13000 indels and a similar number of somatic variants, so it's very unlikely none are in gene regions. Using ht19 for txdb. Thanks for any tips!

R Bioconductor VariantAnnotation Indel • 715 views
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