Introduction to the Genome STRiP software.

Data bundles for commonly used reference genomes, needed for using Genome STRiP.

General information on the Queue workflow engine and how to run Queue scripts.

Architecture of the Genome STRiP 2.0 CNV pipeline.

Architecture of the Genome STRiP 2.0 large/somatic CNV pipeline.

The command line interface to Queue and a description of the common pipeline arguments.

The SVPreprocess Queue script performs common processing steps on the input data that are required for all other Genome STRiP pipelines.

The SVDiscovery Queue script implements the original Genome STRiP deletion discovery pipeline.

The SVGenotyper Queue script supports genotyping of structural variant sites.

The CNVDiscoveryPipeline is a Queue script for CNV discovery and genotyping.

The LCNVDiscoveryPipeline is a Queue script for detecting large/mosaic CNVs from read depth.

Annotation engine and framework for SV annotation.

Annotator that calculates summary statistics on population allele frequency and Hardy-Weinberg equilibrium.

Annotator that reports on the separation of read depth clusters used in genotyping.

Annotator that report statistics about the distribution of copy number states at each variant.

Annotator that calculates local GC content for structual variants.

Annotator used to detect and report overlaps between structural variations and annotated genes.

Annotator for performing "in silico" validation of copy number variants using SNP array intensity data.

Annotator used to detect and filter sites that are likely not polymorphic in the genotyped population.

Annotator for computing reciprocal overlap between sets of structural variants.

Annotator used to detect and filter redundant structural variation calls with similar coordinates.

Annotator that evaluates tagging SNPs (or other markers) based on pairwise r².

Annotator that reports on the distribution of variant calls across samples.

Combine multiple CNV sites into longer structural haplotypes based on composite genotype likelihoods.

Generate genotype likelihoods for inferred copy number alleles based on diploid copy number likelihoods.

Make plots to visualize the genotyping data for individual variants.

Make haplotype spider plots for phased variants.

Utility Queue script used to prepare data for the LCNV discovery pipeline.