Search Results for "somatic"
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Showing 30 open source projects for "somatic"
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hg38 version of the pipelines for whole exome sequencing: exome_test38.sh wole transcription sequencing: rna_test38.sh somatic calling: somatic38.sh SV detect: svdetect38.sh, meerkat38.sh cnv: svdetectcnv38.sh, contra38.sh, cnvkit38.sh *** Mutect2 instead of haptotypecaller is used to call variants in DNA-seq.
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somatic.sh
script for somatic SNP and Indel calling
somatic.sh is a shell script to run varscan somatic for somatic variant-calling, and Annovar to annotate. It calls both SNPs and Indels. It also produces 2 MAF files compatible with MutSigCV. Now the script allows for multithreading. The script is updated according to new format. -
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GASOLINE
Germline And SOmatic structuraL varIants detectioN and gEnotyping
GASOLINE is a collection of Perl, R and Fortran codes for the detection of germline and somatic SVs from long read sequencing data. -
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PhaseDel
Phasing-based somatic deletion caller from single-cell WGS data
...The important features of PhaseDel are: • Accurate identification of somatic focal deletions at single-base-pair resolution in scWGS using phasing information • Estimation of the genome-wide somatic deletion rate for a given cell with the controlled FDR level • Characterization of underlying DSB repair mechanisms for identified deletion candidates A more detailed description of the tool is provided in the [[wiki]] tab. -
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SingleCellSeqCNV
Detection of Copy Number Alterations by Single Cell Sequencing
Detection of Copy Number Alterations by Single Cell Sequencing Kristin A. Knouse, Jie Wu and Angelika Amon, Assessment of megabase-scale somatic copy number variation using single cell sequencing. Genome Research, 2016. gr. 198937.115 Kristin A Knouse, Jie Wu, Charles A Whittaker and Angelika Amon. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proceedings of the National Academy of Sciences, 2014. 111(37):13409-13414. -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc... -
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Somatic APP analysis
Reanalysis of somatic APP retrotransposition
Implemented code for the reanalysis of somatic APP retrotransposition originally claimed by Lee at el (Nature, 2018). Modules for two different analyses--detection of intra-exonic junctions (IEJs) and estimation of APP gencDNA fraction--are provided. A detailed description of our analysis is available in our bioRxiv paper (https://bit.ly/35Kgfbu). [ Basic usage ] • Detection of IEJs connecting APP exons java -jar somaticAPP.jar -D -b input.bam [optional_arguments] * Input data: PRJNA577966 * The input bam should be mapped to APP751.fa (provided in the 'data' folder) and sorted by read name after mapping • Estimation of gencDNA fraction java -jar somaticAPP.jar -F -b input.bam -a BWA_PATH -s SAMTOOLS_PATH [optional_arguments] * Input data: PRJNA493258 * The input bam should be a human-genome-mapped (hg38), coordinate-sorted, and duplicate-marked file. ... -
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RePlow
Replicate-based caller for the accurate detection of low-frequency SNV
RePlow is a Java based variant caller designed for detecting somatic single nucleotide variants (SNVs) from the replicated set of high-depth sequencing data. RePlow is highly specialized for the identification of somatic mutations with low variant allele frequency (VAF ~1%). RePlow accurately detects such low-level mutations based on the probabilistic model that jointly analyzes library-level replicates, regardless of the sequencing platform. -
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers. The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. ... -
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NanoGLADIATOR
Real-time detection of copy number alterations from nanopore data.
...In "On-line" mode the tool must be launched simultaneously to a nanopore experiment so that, by exploiting the data flow generated during the sequencing process, it can perform real-time CNVs/CNAs detection. In "Off-line" mode Nano-GLADIATOR can be used to perform parallelized analysis of multiple runs at once for the identification of germline CNVs and somatic CNAs. -
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Nuvarator
A SNV Detection Software Tools Installer Package
A software package Nuvarator which downloads and installs different tools related to Somatic SNV detection. SNV detection is range of computational tech- niques and algorithms used to identify the existence of single nu- cleotide variants (SNVs) by using the result from Next Generation Sequencing (NGS) experiments. NGS are methods employed for Whole Genome Sequencing, a process for determining the precise order of nucleotides within a DNA molecule which can improve the knowledge available to researchers interested in evolutionary biology, and hence lays the foundation for predicting disease susceptibility and drug response. ... -
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scalpel
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads. -
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AIRVF was developed to increase accuracy of low-frequency variant calling. Our zip file contains programs for both Window and Linux. AIRVF demonstrated higher precision and sensitivity by accurately detecting SNVs with low VAF in Ion Torrent data. If you cannot install Torrent Suite in non-Ubuntu Linux servers, the AIRVF and VarScan2 pipeline can be a good alternative. But combination of SNVs from VarScan2 and indels from Torrent Variant Caller-Ion Reporter will demonstrate the best...
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novoBreak
Robust detection of somatic structural breakpoints in cancer genomes
novoBreak is a tool used in cancer genomic studies to discover SV (both somatic and germline) breakpoints. It can report accurate breakpoints of Deletions (DEL), Duplications (DUP), Inversions (INV) and Translocations (TRA) (you should consider some of them are mobile elements insertions or templated insertions). For novel insertions, we may only report the breakpoints but not the inserted sequence. Please forget about novel insertions at the moment. -
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Edesign
Primer and enhanced internal probe design tool
... - Functions for designing internal probes are greatly enhanced. - "Genotyping mode" provides design of the internal probe over a user-specified target variant e.g. (SNP, insert/deletion, somatic mutation etc) for genotyping. - Modified oligonucleotide can be designed. The original Edesign treats Eprobe and Eprimer. For technical support please contact: contact@dnaform.jp -
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Vecuum
Contamination-induced false variant caller
NEWS: 02-08-16 A new version of Vecuum 1.0.1 has been uploaded. Kim J et al, "Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination", Bioinformatics (2016): btw383. http://bioinformatics.oxfordjournals.org/content/early/2016/07/12/bioinformatics.btw383 Vecuum is a Java based variant caller designed for detecting contamination-induced point mutations from hybrid-capture-based genome sequencing data (e.g. -
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A machine learning-based method for somatic variant identification from low-pass next-generation sequencing.
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The IntSim software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity.
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SCNVSim
SCNVSim, a tool to simulate somatic CNV and Strucuture Variants
SCNVSim is a Bioinformaitcs tool developed in Java programming language for the simulation of somatic copy number variations and structure variations in cancer genome studies. The tool is capable of simulating features related to tumor samples including tumor purity, aneuploidy and heterogeneity other than common types of SV and CNV. SCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterogeneity, and structure variation break points, which are essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies. -
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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Virmid
Virtual Microdissection for SNP calling
...While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: •Estimation of accurate proporation of control sample in a (mixed) disease sample •Improved SNP and somatic mutation calling with regard to the estimated proportion -
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oasis-genomics
Oasis Genomics cancer omics integration portal
OASIS is an application that enables complex analytical queries across somatic mutations; copy number changes (CNV); and gene expression data. OASIS has been built on top of the BIoMart frameworks and has been extended to incorporate unique tools and visualizations to facilitate analysis of complex cancer "Omics" datasets. -
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SoloDel
Somatic Low-frequent Deletion Caller Model
SoloDel (Somatic Low-frequent Deletion call model) is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples. The important features of SoloDel are: • Estimation of mutational frequency in a mixed disease sample without matched control • Improved somatic deletion calling based on the probabilistic model with the parameter estimation -
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Ever wanted to predict Copy Number Variants from your Exome data? Here is CNVler, a tool which is able to predict CNVs in Parent-Child trios, tumor-normal pairs (somatic) and population (germline).
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RAREVATOR
Tool for the detection of variants in rare reference allele loci
RAREVATOR (RAre REference VAriant annotaTOR) is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data. RAREVATOR has been published on BMC Genomics. Magi A, D'Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF. Characterization and identification of hidden rare variants in the human genome.
