Search Results for ".vcf" - Page 2
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Showing 61 open source projects for ".vcf"
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. ... -
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VCFZip
VCFZip is a compression tool for VCF files.
VCFZip can compress a VCF file with higher compression ratio than gzip and BCF. It is designed to store full information in a VCF file with minimum disk space. -
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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vcfhacks
simple to use commandline programs for VCF filtering and manipulation
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/vcfhacks) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/vcfhacks/releases/latest). (relatively) Simple to use commandline tools for the manipulation and analysis of VCF files, geared towards the identification of pathogenic mutations in Mendelian disease. -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes... -
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
...This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. These informative variants have been established by comparing allele frequencies between strain-types using ancestral node comparisons and FST measures of population differentiation. -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
...Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf files as an input file, our program identifies the majo -
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Athus
Manage, merge, filter and convert population genetics data
This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina call files) * work with genetic maps ... -
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snpSniffer
snpSniffer is a sample integrity checking tool for NGS data
...It ensures no sample mixups have occurred by checking genotype concordance of carefully curated genomic loci. It currently works on whole genome, exome and RNA-Seq data. Identifying mixups involves 3 steps 1. Generate the genotypes in a vcf format at specific genomic loci 2. Adding the genotypes generated to a flat file "database.ini" provided 3. Compare the genotypes for samples of interest, examine the snpSniffer output and infer if any mixups occurred All the above steps can be run using snpSniffer -
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vcards
busca dentro de archivo vcf y crea tantos archivos como contactos hay
se configura el directorio donde guardar los archivos creados, (deben existir), basicamente busca dentro del archivo vcf la cadena BEGIN, si la encuentra crea un archivo limitado a 6 lineas luego del begin, luego busca en ese archivo la cadena END, si no la encuentra vuelve a buscar en el archivo vcf esta ves con una linea mas, asi hasta que encuentre la linea END, luego crea un archivo llamado desde Tn, vcf hasta Tnnn.vcf la busqueda esta limitada a 226 resultados, se debe ajustar las variables para casos concretos, se podria usar para buscar cadenas de texto delimitadas en cualquier tipo de archivo, realizando las modificaciones pertinentes -
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Andoffline
A toolkit for some Android sms/call Apps, base64 encoder, vcf parser a
MOVED TO: https://github.com/fulvio999/Andoffline Feature: Browser for exported SMS, CALL and CONTACT from Android Phone Save to PDF file for exported SMS, CALL and CONTACT, VCF parser Support tool for: http://android.riteshsahu.com/apps/sms-backup-restore http://android.riteshsahu.com/apps/call-logs-backup-restore Image base64 encoder/decoder ** Allow to execute job/script execution from SMS sent from remote phone (without internet connection): - connect the phone to PC with usb - Install the Android App - create a job on desktop application - start PC listener and Phone receiver ** See pdf guide for more details - web application to manage job/script stored in a relational DB (Mysql or sqlite). ... -
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H3M2
H3M2: Detection of ROH from whole-exome sequencing data
...We recently published on Computational and Structural Biotechnology Journal (CSBJ) a novel software package, named AUDACITY, for the identification of Runs of Homozygosity by using VCF files from whole-exome and whole-genome sequencing data generated by second generation sequencing technologies. (https://www.sciencedirect.com/science/article/pii/S2001037020303354). AUDACITY is freely available at https://sourceforge.net/projects/audacity-tool/. H3M2 is novel computational approach for the identification of Runs of Homozygosity by using whole-exome sequencig data generated by second generation sequencig technologies. ###################################################################### The H3M2 algorithm has been published on Bioinformatics. ... -
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vcf2MSAT
Find Microsatellites in a ".vcf" report
vcf2MSAT is a python program to identify microsatellite repeat regions based on known polymorphisms identified in a ".vcf" report after using SAMtools to analyze next-generation sequencing files. -
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VCFannotator
Annotate SNPs in the context of Gene Annotations
A VCF file is parsed to identify genomic variations, and these variations are placed in the context of genome feature annotations. In the case that a mutation is coding, the type of coding mutation and impact on the protein-coding sequence is indicated. -
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rcard
ncurses VCard 3.0 contact management editor
A vcard 3.0 contact management editor developed for ncurses. It can: - load a vcf file - show all the contacts in a list - show more information about a single contact - perform a simple search in the contacts list - edit contacts - support UTF-8 (currently not on WIN32, though I'm not sure WIN32 console is actually able to support UTF-8) - convert the VCF(s) to Pine/Alpine addressbook format - import images from files as contacts photos The idea is based upon rolo (which you can find at SourceForge.net, too), but no original code remains. ... -
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PhonixJ
A cross-platform phone-book written in Java using SWT.
...Features: - Add/remove contacts - Create vCard v.3.0 - Create Contact Card in .SVG - Create mail envelope address - Sophisticated search engine - Customizable printing options - Support for email and browser clients - Batch export/import of the contacts via .vcf (3.0) files (tested with Kontact) - A tool to select multiple e-mail addresses, copy them to clipboard and open compose mail Current version: 1.0.3 News: - Added notes record to each contact - If you want to see it in your own language, please download the Main.properties, and translate it, then send it back to me. Please contact me if you'd help, and specify your special needs if any. -
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QR Gen
Multi-platform QR code generator from information supplied
QRGen creates QR codes from contact information, written in Java. It requires the tool qrencode in order to work, qrencode is freely available at http://fukuchi.org/works/qrencode (Linux/Mac OS/UNIX) , or http://code.google.com/p/qrencode-win32/ (Windows), or Ubuntu Software Centre. -
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ligth-genome-view
small genome viewer local wxWidget c++
...I am a newbie in bioinformatics. Hope this will give people help when build bio-GUI project using c++. This software is used to view genome including many type files,like bed,gff,gtf,vcf,fasta,bam. -
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Super-Alias Virtual Digital
Super-Alias Virtual Digital: simulation of digital audio artefacts
Super-Alias Virtual Digital: Simulation of artefacts in legacy digital audio equipment. Includes the following modules: variable quantization, vari-speed, variable re-sampling and aliasing, aperture, jitter, brick-wall band-pass filtering, and VCF. Copyright (c) 2008-2013 by Klaus Michael Indlekofer. All rights reserved. Note: Special restrictions apply. See disclaimers below and within the distribution. (We are not affiliated in any way with companies/persons mentioned above. All brand names and trademarks are property of their respective owners.) -
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dbVcfSplitter - vCard Splitter
vCard file splitter
You can export Google contacts and import to your Nokia phones very easily. Just export the Google contacts in vCard format (.vcf file). Split the file using "dbVcfSplitter" and import those files using your Nokia PC Suite or OVI Suite. Done!! Usage: (1) Open the Command Prompt or the terminal. (2) "cd" to the folder/directory where the .vcf file resides. (3) type as shown below java -jar dbVcfSplitter.jar filename.vcf -
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vcf2csv
(abandoned and outdated project) convert vcard data into csv format
vcf2csv is a command line tool, written in ANSI-C (C90), converts a vcard (vcf) file to csv. Please note: the ability to generate HTML-files will be removed in the near future. -
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Shows you all VCF files, that are inside chosen folder. You can view and read them, nothing more (at least now).
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Translate VCF
Determine functional consequences of mutations in a vcf file
Takes vcf file input and determines functional consequence of mutations with regard to UCSC known genes, refseq genes or ensembl genes. Will use UCSC known gene annotation by default. A correctly formatted CDS file must be used containing CDS sequences and gene table info (i.e. info from knownGene.txt for UCSC genes, refGene.txt for RefSeq or ensGene.txt for ensembl as downloaded from the UCSC downloads page [http://hgdownload.cse.ucsc.edu/downloads.html or ftp://hgdownload.cse.ucsc.edu/]) for the relevant gene set. ... -
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This is a simple program that allows you to get the information in a vCard file (.vcf) as plain text. vCards are used to store contact information and may be created by Apple's Address Book and other similar programs, along with mobile phones.
