Genome STRiP Cookbook

On this page, we have collected a set of example recipes for performing analyses using Genome STRiP.

Installation

Installing Genome STRiP

Genotyping

‚ÄčGenotyping a novel site using 1000 Genomes Phase 1 (local)

This recipe demonstrates how to assess a novel site (or a small number of novel sites) using the 1000 Genomes data. This recipe is useful if you have a suspected large deletion variant and want to know if there is any evidence for this variant in the 1000 Genomes populations, and if so, what is the population distribution. This recipe uses a local installation of Genome STRiP but runs against a remote copy of the 1000 Genomes data.

Genotyping a novel site in 1000 Genomes Phase 1 using AWS

This recipe demonstrates how to use the Amazon Cloud to run the same scenario as above: Genotyping a novel site (or a small number of novel sites) using the 1000 Genomes data. This recipe takes advantage of the public AWS data set containign the 1000 Genomes data.

Amazon Web Services (AWS)

Running Genome STRiP on the Amazon cloud

This recipe explains the basics of how to install and configure GenomeSTRiP to run on the Amazon cloud. Once you have created an AWS cluster configured to run Genome STRiP, most Genome STRiP processing pipelines can be run on the cloud.