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It seems something odd in VEP itself:
1:g.23688489_23688499delAATAAGAGCTGinsTT
1:g.23688489_23688499delAATAAGAGCTGinsT
These two variants actually all result in S459*, but VEP calls the first one as stop gained, but the second as frameshift.
Describe the bug
Bug 1: A nonsense indel in Jannovar is annotated as frameshift_variant. VEP also calls it frameshift_variant. However, pdots are not the same.
For example,
annotate-var/refseq/hg19/chr1/197071665/AGTTT/A
VEP results
VEP indicates p. should be
p.Lys2238Ter
while Jannovar returnsp.(K2238fs)
Bug 2: Nonsense indel gets
disruptive_inframe_deletion
from Jannovar butstop_gained
from VEP.For example,
annotate-var/refseq/hg19/chr8/38277141/CTTG/C
VEP results:
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