Genome STRiP

Description

genomestrip website  

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.

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. A minimum of 20 to 30 genomes are required to get acceptable results, but the method gains power across genomes and processing more genomes 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.

Required Modules

Serial

• genomestrip

System Variables

• HPC_{{#uppercase:genomestrip}}_DIR - installation directory

Additional Information

Genome STRiP meta data is located in /scratch/lfs/bio/reference/genomestrip

• HPC_GENOMESTRIP_META - metadata directory

Citation

If you publish research that uses genomestrip you have to cite it as follows:

Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA Large multiallelic copy number variations in humans Nature Genetics 47, 296-303 (2015) PMID: 25621458