Stanford Medicine

Variant Analysis

Sequence To Medical Phenotypes

Sequence to medical phenotypes (STMP) is an open source, parallelized pipeline for identifying clinical phenotypes in whole genome and whole exome sequence data generated in a research setting. It is highly amenable to parallel processing architecture, produces parsimonious variant sets for manual review, and interrogates both Mendelian disease risk, in target gene lists or genome wide, and genetic drug response.

The overall heuristic is described in this figure.

Source code is available at: https://github.com/AshleyLab/stmp