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SV-STAT / Structural Variation detection by STAck and Tail

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Quantifies evidence for structural variation in genomic regions suspected of harboring rearrangements. SV-STAT extends existing methods by adjusting a chimeric read’s support of a structural variation by (i) the number of its soft-clipped bases and (ii) the quality of its alignment to the junction. SV-STAT is more accurate than alternative methods for determining base-pair resolved breakpoints. SV-STAT is a significant advance towards accurate detection and genotyping of genomic rearrangements from DNA sequencing data.

forestSV

Integrates prior knowledge about the characteristics of structural variants (SVs). forestSV is a statistical learning approach, based on Random Forests (RFs) that leads to improved discovery in high throughput sequencing (HTS) data. This application offers high sensitivity and specificity coupled with the flexibility of a data-driven approach. It is particularly well suited to the detection of rare variants because it is not reliant on finding variant support in multiple individuals.

cn.MOPS / Copy number estimation by a Mixture Of PoissonS

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.MOPS. It models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.MOPS decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively.

SVTyper

New
Assists users to infer an underlying genotype at each structural variants (SVs). SVTyper is a Bayesian likelihood algorithm that can operate on copy-neutral events such as inversions and translocations as well as copy number variants (CNVs). It permits the production of SV genotypes, useful for meaningful variant interpretation, as well as quantitative estimates of breakpoint allele frequencies that allow inference of the fraction of tumor cells that carry a particular variant.

MATE-CLEVER / Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder

An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios or quartets, MATE-CLEVER integrates statistics that reflect the laws of Mendelian inheritance. MATE-CLEVER's performance rates for indels longer than 30 bp are on a par with those of the GATK for indels shorter than 30 bp, achieving up to 90% precision overall, with >80% of calls correctly typed. In predicting de novo indels longer than 30 bp in family contexts, MATE-CLEVER even raises the standards of the GATK.

PEMer

A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. The package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from the ‘novel’ genome. Subsequent analysis with PEMer workflow on the simulated reads can facilitate parameterize PEMer workflow. BreakDB is a web accessible database developed to store, annotate and dsplay SV breakpoint events identified by PEMer and from other sources.

SWAN / Statistical Structural Variant Analysis for NGS

A statistical framework and algorithm for structural variant (SV) detection from whole genome sequencing data. SWAN integrates multiple features, including insert size, hanging read pairs and read coverage into one statistical framework and detects putative SVs through genome-wide likelihood ratio scans. SWAN remaps soft-clip/split read clusters to supplement the likelihood analysis, joins multiple sources of evidence and identifies break points whenever possible. SWAN has improved sensitivity for detecting structural variants smaller than 10 kilobases and is particularly successful at identifying deletions smaller than 500 base pairs.

VarDict

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict contains many features that are distinct from other variant callers, including linear performance to depth, intrinsic local realignment, built-in capability of de-duplication, detection of polymerase chain reaction (PCR) artifacts, accepting both DNA- and RNA-seq, paired analysis to detect variant frequency shifts alongside somatic and loss of heterozygosity (LOH) variant detection and structural variant (SV) calling. VarDict facilitates application of next-generation sequencing in cancer research, enabling researchers to use one tool in place of an alternative computationally expensive ensemble of tools.

PSSV

A probabilistic method for somatic structural variation (SV) prediction by jointly modeling discordant and concordant read counts. PSSV is specifically designed to predict somatic deletions, inversions, insertions and translocations by considering their different formation mechanisms. Simulation studies demonstrate that PSSV outperforms existing tools. PSSV has been successfully applied to breast cancer data to identify somatic SVs of key factors associated with breast cancer development.

inGAP-sv

Detects and visualizes structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important features, including local depth of coverage, mapping quality and associated tandem repeat, are used to evaluate the quality of predicted structural variation. Compared with other approaches, it can detect many more large insertions and complex variants with lower false discovery rate. Moreover, inGAP-sv, written in Java programming language, provides a user-friendly interface and can be performed in multiple operating systems.

JointSLM

An algorithm that extend the univariate SLM to the multivariate case in order to detect recurrent shifts in the mean of multiple sequential processes. The resolution of JointSLM strictly depends on the signal to noise ratio (SNR) of the data: increasing the SNR of DOC data by reducing the sequencing error rate or augmenting the coverage of the sequencing experiments, will improve the performance of JointSLM in detecting small shifts in the signals. The JointSLM algorithm can be also used to analyse multiple tumour samples data for the discovery of recurrent copy number alterations.

Sniffles

Provides a structural variation (SV) caller for long reads. Sniffles is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations). Sniffles can detect all of these types and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication). Furthermore, Sniffles incorporates multiple auto tuning functions to determine data set depending parameter to reduce the overall risk of falsely infer SVs.

SVelter

Identifies regions of the genome suspected to harbor a complex event. SVelter then resolves the structure by iteratively rearranging the local genome structure, in a randomized fashion, with each structure scored against characteristics of the observed sequencing data. SVelter is able to accurately reconstruct complex chromosomal rearrangements when compared to well-characterized genomes that have been deeply sequenced with both short and long reads. SVelter is able to interrogate many different types of rearrangements, including multi-deletion and duplication-inversion-deletion events as well as distinct overlapping variants on homologous chromosomes.

readDepth

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. It can also be used to infer copy number using reads obtained from bisulfite sequencing experiments.

BreaKmer

forum (1)
An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants.

Sprites

Finds deletions from sequencing data. Sprites aligns a whole soft-clipping read rather than its clipped part to the target sequence, a segment of the reference which is determined by spanning reads, in order to find the longest prefix or suffix of the read that has a match in the target sequence. This alignment aims to solve the problem of deletions with microhomologies and deletions with microinsertions. Using both simulated and real data we show that Sprites performs better on detecting deletions compared to other current methods in terms of F-score.

TrioCNV

A tool designed to jointly detecting copy number variations (CNVs) from whole genome sequencing data in parent-offspring trios. TrioCNV models read depth signal with the negative binomial regression to accommodate over-dispersion and considered GC content and mappability bias. It leverages parent-offspring relationship to apply Mendelian inheritance constraint while allowing for the rare incidence of de novo events. It uses a hidden Markov model (HMM) by combining the two aforementioned models to jointly perform CNV segmentation for the trio.

SV-Bay

Detects structural variants in cancer using whole genome sequencing data with or without matched normal control sample. SV-Bay does not only use information about abnormal read mappings but also assesses changes in the copy number profile and tries to associate these changes with candidate SVs. The likelihood of each novel genomic adjacency is evaluated using a Bayesian model. In its final step, SV-Bay annotates genomic adjacencies according to their type and, where possible, groups detected genomic adjacencies into complex SVs as balanced translocations, co-amplifications, and so on. A comparison of SV-Bay with BreakDancer, Lumpy, DELLY and GASVPro demonstrated its superior performance on both simulated and experimental datasets.

Manta

Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and large insertions within a single workflow. The method is designed for rapid analysis on standard computer hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, most WGS tumor-normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in individual diploid samples and somatic variants in matched tumor-normal sample pairs.