Why snpEff annotates same region with different "effects" and why some effects are given in combination? What is the criteria to filter this annotation?
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15 months ago
svp ▴ 450

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

snpEff VEP VariantAnnotation Exome VCF • 473 views
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well, if the variant is a deletion overlapping a splice junction, it fulfills all the conditions above.

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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?

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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.

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

splice_donor_variant&missense_variant&disruptive_inframe_deletion&splice_region_variant&intron_variant

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

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