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[], 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!