GotCloud: GenomeSTRiP Pipeline

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GenomeSTRiP

GenomeSTRiP was developed at the Broad Institute and at the McCarroll Lab at the Harvard Medical School Department of Genetics: http://www.broadinstitute.org/software/genomestrip/

If you use GenomeSTRiP for your research, please cite it:

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

GenomeStrip is currently included within GotCloud and can be run through GotCloud.

Why use GenomeSTRiP?

1. GenomeSTRiP is a mature software for detecting and genotyping large deletions (and duplications soon to be implemented). In 1000 Genomes, GenomeSTRiP was demonstrated as one of the top-performing SV caller in most evaluation metrics.
2. GenomeSTRiP is a great tool to integrate across multiple structural variant calls. When multiple structural variant calls exists, all the other variants can be genotyped and filtered with GenomeSTRiP, and that is how 1000 Genomes structural variant call sets were made.
3. Currently, GenomeSTRiP only allows calling large deletions, but duplicate calling pipeline is under way.

Why do we use GotCloud/GenomeSTRiP pipeline?

1. The main purpose of GotCloud pipelines is to provide a pipeline for users with limited knowledge and experience with high performance computing environment.
   • GotCloud/GenomeSTRiP provide a simple interface consistent to alignment, SNP, and indel calling.
   • GenomeSTRiP itself also provides a straightforward pipeline to use as standalone software
2. GotCloud supports a variety of cluster environment that is not currently supported by GenomeSTRiP
   • GenomeSTRiP is designed based on a framework called Qscript, which provide a nice support for LSF cluster system
   • GotCloud support many additional cluster environments such as MOSIX or SLURM we use locally at Michigan.
3. GotCloud also provide a fault-tolerant solution for large-scale jobs.
   • GotCloud automatically picks up jobs from the point where it failed. This allows easier and simpler run against potential technical glitches in the system.

Overview of GotCloud/GenomeSTRiP pipeline

GotCloud/GenomeSTRiP pipeline consists of three separate steps.

• Preprocess step : Create metadata summarizing the GC profiles, depth distribution, insert size distribution for accurate discovery and genotyping of structural variants.
• Discovery step : Perform variant discovery split by region, across all samples. Also, perform variant filtering based on expert knowledge.
• Genotyping step : Iterate discovered variants across the samples and calculate the genotype likelihood of for each possible genotype.

In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.

• Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.