How does Emedgene Analyze prioritize transcripts?
Last updated
Was this helpful?
Last updated
Was this helpful?
Emedgene uses VEP and EFF for transcript annotations and in upcoming versions will be adding Illumina Connected Annotations.
Each variant has a "main_effect" and "main_gene" chosen based on the most prioritized transcript for this variant. Transcript prioritization depends on many different parameters and on different Emedgene pipeline versions.
Here is a list of ordered rules for transcript prioritization:
VEP transcripts are prioritized over EFF transcripts.
If the case is a virtual panel, prioritize transcripts from genes in the case gene list (but not for Boosted Genes type panels).
Prioritize RNA genes associated with disease (See for prioritized list RNA genes). Importantly this does not apply to upstream and downstream RNA variants.
De-prioritize transcripts.
Prioritize based on in the following order: HIGH > MODERATE > LOW > MODIFIER.
Prioritize introns over UTR over upstream (.
Prioritize organization canonical transcripts (. Always applied, no settings needed).
Prioritize canonical transcripts (Based on ).
Prioritize transcripts from genes in the case gene list.
Prioritizing gene without “-” in their Name.
Here is a list of ordered rules for transcript prioritization:
VEP transcripts are prioritized over EFF transcripts.
If the case is a virtual panel, prioritize transcripts from genes in the case gene list (but not for Boosted Genes type panels).
Prioritize RNA genes associated with disease (See for prioritized list RNA genes). Importantly this does not apply to upstream and downstream RNA variants.
De-prioritize transcripts.
Prioritize based on in the following order: HIGH > MODERATE > LOW > MODIFIER.
Prioritize introns over UTR over upstream (.
Prioritize organization canonical transcripts (, this parameter has to be implemented upon request.).
Prioritize canonical transcripts (Based on ).