Search Results for "cnv"
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Showing 19 open source projects for "cnv"
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ParseCNV CNV call association software takes CNV calls as input and creates SNP based statistics for CNV occurrence in population study cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
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Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
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CNVision
CNV prediction from Illumina genotyping data
CNVision is a Perl script that runs Illumina genotyping data (all chips from 300k to latest Omni) through PennCNV, QuantiSNPv2.3 and GNOSIS (an in-built algorithm). It merges the results and assesses the quality of the raw data. CNVision can also identify de novo CNVs in family-based data using a highly accurate algorithm that considers the possibility of CNVs in either parent based on the raw genotyping data. The script is optimized to work in a UNIX-based environment; it should work in... -
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ADTEx
Aberration detection in tumour exome
Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. -
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cnvCapSeq
detecting & genotyping CNV in long-range targeted resequencing.
cvnCapSeq is a set of Java-based command-line tools for detecting and genotyping copy number variation (CNV) in targeted resequencing experiments of large contiguous genomic regions. -
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Magnolya
De novo CNV detection by co-assembly
Magnolya enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets. -
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
...A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of heterozygosity (LOH) events in Candida albicans, the most common human fungal pathogen, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains. ... -
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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noise-free-cnv
program for analyzing and manipulating DNA microarray data
CNV calling software may produce false-positive calls due to imperfect source material. Direct inspection of the microarray data with the noise-free-cnv software helps to appreciate the quality of the data and to identify artificial calls. With noise-free-cnv it is possible to visualize individual datasets, to compare different datasets and to perform simple transformations. -
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bint
Converts intensity text files to binary for fast subsetting
bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow grep/awk'ing the text files exported from the genotyping run (e.g. Illumina final report files). bint converts the text representation of the intensity float data to into a IEEE754 indexed binary file for rapid extraction of subsets of the data. ... -
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GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of intensity data. It is powerful and sensitive in detecting small CNV associations, and retains high power for large CNVs.
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The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
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AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data.
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CNV-WebStore is an integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Contact system admin at http://cnv-webstore.uantwerpen.be for installation scripts
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CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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Collection of tools for performing robust case-control disease and quantitative trait association studies using Copy Number Variants- Latest version should now be downloaded from Bioconductor
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cel2fr
Tool to convert Affy cel files to be Illumina Final Report compatible
cel2fr is a perl script that can be used to convert Affymetrix CEL files into a format matching an Illumina Final Report. The primary use of this tool is to work in concert with the CNV analysis tool CNVision (www.cnvision.org), but its use is ideal for meta-studies combining multiple datasets. Current version is not yet functional.
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