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Old 04-22-2015, 03:08 AM   #1
Nilaksha
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Location: Sri Lanka

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Default snpeff canonical transcript annotations: multiple annotations problem

Hi,
I'm using snpEff in my exome sequencing pipeline and I use -canon option to get only the canonical transcripts annotated for a particular variant. But eventhough I'm using the option, I can see there are multiple annotations for a single variant in the INFO field of the vcf file.

1 2488153 . A G . . NS=1;AN=2;AC=2;ANN=G|missense_variant|MODERATE|TNFRSF14|ENSG00000157873|transcript|ENST00000355716|protein_coding|1/8|c.50A>G|p.Lys17Arg|349/1707|50/852|17/283||,G|sequence_feature|LOW|TNFRSF14|ENSG00000157873|signal_peptide|ENST00000355716|protein_coding|1/8|c.50A>G||||||,G|sequence_feature|LOW|TNFRSF14|ENSG00000157873|signal_peptide|ENST00000355716|protein_coding|2/8|c.50A>G||||||,G|intragenic_variant|MODIFIER|RP3-395M20.8|ENSG00000238164|gene_variant|ENSG00000238164||||||||| GT:PS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGLP:AD:CGA_RDP 1/1:.:PASS:30:179,30:179,30:44,28:-179,-30,0:-44,-28,0:11:11,11:0

Can somebody explain this to me please.

Thanks in advance.
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Old 03-21-2017, 09:16 AM   #2
AChristofferson
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Location: Phoenix, AZ

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Default

I am seeing the same thing almost two years later and can't seem to make sense of it.
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