Overview

Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals, but can also process single genomes.

Genome STRiP looks both across and within a set of sequenced genomes to detect variation. The methods are adaptive and support heterogeneous data sets, including variations in sequencing depth, read lengths and mixtures of paired and single-end reads. Typically 20 to 30 genomes are required to get good results, but the method gains power across genomes and more genomes will provide better results.

To run discovery or genotyping on a single sequenced genome or a small set of genomes, you need to call your data against a background population, such as a set of genomes from the 1000 Genomes Project.  The background population does not need to be matched to the target individuals.

Genome STRiP can be used for discovery of novel structural variations or to genotype known variants in new samples.

Citing Genome STRiP

Please use the following reference to cite Genome STRiP

Handsaker RE, Korn JM, Nemesh J, McCarroll SA
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Nature genetics 43, 269-276 (2011)
PMID: 21317889