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GEMINI pathways (version 0.20.1)

GEMINI database:

Only files with version 0.20.1 are accepted.

Version of ensembl genes to use:

Supported versions: 66 to 71. Use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)

Report only pathways with loss-of-function variants:

(--lof)

Choose a gemini annotation source:

What it does

Mapping genes to biological pathways is useful in understanding the function/role played by a gene. Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases. We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.

This requires your VCF be annotated with either snpEff/VEP.