Question: Why snpEff annotates same region with different "effects" and why some effects are given in combination? What is the criteria to filter this annotation?
gravatar for svp
7 months ago by
svp420 wrote:

snpEff annotates same region for different effects. But how does it make a combination of prediction within the same transcript as follows:


For example transcript enst1234 is enriched with splice_donor_variant&missense_variant&disruptive_inframe_deletion&splice_region_variant&intron_variant. How this is been done. How can I filter the variants from this combination as this is given as one effect

ADD COMMENTlink written 7 months ago by svp420

well, if the variant is a deletion overlapping a splice junction, it fulfills all the conditions above.

ADD REPLYlink written 7 months ago by Pierre Lindenbaum133k

How can I filter single effect when multiple effects are given in combination. What is actual criteria for giving combination of effect as one effect?

ADD REPLYlink written 7 months ago by svp420

I don't think you can do this. There should be a one and only term to define this in gene_ontology) . I think it's more a problem on your side (how to grep for a consequence with multiple terms) than finding the right term in SO.

ADD REPLYlink written 7 months ago by Pierre Lindenbaum133k

I did not get your point. Can you give me an example with following data to identify correct SO term


For above enriched term, what is the single SO term?

ADD REPLYlink written 7 months ago by svp420
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