<aside> 💡 Personal download links with results are sent to provided email so it is vital that the correct e-mail is submitted by user. Results are available for download for 30 days since creation.
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All the jobs require a job name, user e-mail, input (format described in the 3 subsequent sections, see below) and human assembly version used for input genomic coordinates: GRCh37/hg19 or GRCh38/hg38.
Users can take 3 different routes depending on their input into MendelVar.
In Route 1, user provides a list of pre-defined intervals
In Route 2, user provides a list of single positions which are then expanded to intervals using custom fixed left and right flanks, up to 10 Mbp in either direction
In Route 3, user provides a list of single positions which are then expanded to intervals with boundaries defined by the furthest removed variant meeting a minimum LD threshold. The LD-defined boundaries can be subsequently extended to the nearest recombination hotspot.
Steps shared across the 3 routes then include:
-selection of a target 1000 Genomes population in order to generate SNP density-matching background intervals for enrichment testing
-specification of optional 5' and 3' gene overhangs. The overhangs extend gene definition outside of its CDS, by up to 20 kbp in either direction.
-choice of ontologies and pathways for enrichment testing
