Why snpEff annotates same region with different "effects" and why some effects are given in combination? What is the criteria to filter this annotation?
snpEff annotates same region for different effects. But how does it make a combination of prediction within the same transcript as follows:
frameshift_variant&start_lost&initiator_codon_variant&non_canonical_start_codon
frameshift_variant&stop_retained_variant
splice_donor_variant&missense_variant&splice_region_variant&intron_variant
frameshift_variant&initiator_codon_variant&non_canonical_start_codon
splice_donor_variant&missense_variant&disruptive_inframe_deletion&splice_region_variant&intron_variant
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
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well, if the variant is a deletion overlapping a splice junction, it fulfills all the conditions above.
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?
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.
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?