Filters panel

Understand the variants annotations

## Small variants Annotated for gene consequence using snpEff and then annotated with our collection of regulatory regions

## Structural variants Annotated for gene consequence as - intronic_sv: overlap only introns - exonis_sv: overlap at least 1bp of a gene exon

The final list of candidate variant records is then generated as follows: - Most severe consequence is selected for gene affecting variants, so each variant is reported with 1 gene consequence - Each variant can have multiple regulatory annotations if it overlap multiple regulatory regions

So for example the same variant can appear as multiple records in the candidate vars table: chr1    10000     G    T    5UTR chr1    10000     G    T    enhancer

The filtering process is then applied on these single variants records to be able to finely tune the desired output

Variants filters

Variants filters are applied separately for specific variant group, so that each group of filters act only on the relevant variants. Variants group are defined as follows:

1. splicing

   Variants in splicing site or splicing region (10 bp from exon-intron junctions)

2. missense

3. regulatory regions

   Any variant located in one of the annotated regulatory regions (enhancer, promoter, silencer, insulator)