Genome STRiP documentation

Documentation Index

General Documentation

Genome STRiP Overview

Introduction to the Genome STRiP software.

Reference Metadata Bundles

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

Queue Workflow Engine

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

CNV Pipeline Overview

Architecture of the Genome STRiP 2.0 CNV pipeline.

LCNV Discovery Pipeline Overview

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

Pipelines (Queue Scripts)

QCommandLine

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

SVPreprocess

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

SVDiscovery

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

SVGenotyper

The SVGenotyper Queue script supports genotyping of structural variant sites.

CNVDiscoveryPipeline

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

LCNVDiscoveryPipeline

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

Variant Annotation

SVAnnotator

Annotation engine and framework for SV annotation.

Variant Annotators

AlleleFrequencyAnnotator

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

ClusterSeparationAnnotator

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

CopyNumberClassAnnotator

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

GCContentAnnotator

Annotator that calculates local GC content for structual variants.

GeneOverlapAnnotator

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

IntensityRankSumAnnotator

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

NonVariantAnnotator

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

ReciprocalOverlapAnnotator

Annotator for computing reciprocal overlap between sets of structural variants.

RedundancyAnnotator

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

TagVariantsAnnotator

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

VariantsPerSampleAnnotator

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

Utilities

GenerateHaploidCNVGenotypes

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

PlotGenotypingResults

Make plots to visualize the genotyping data for individual variants.

GenerateDepthProfiles

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