Search Results for ".vcf"
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Showing 57 open source projects for ".vcf"
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vcard program vCardz_i
VCF vcard, XML xcard, JSON jcard;View, Edit, Convert, Export, CSV, QR
...Free multifunction vcard address book program to handle multilingual VCF, XML and JSON vcard files. Use the same vcards from your phone, tablet, iOS, other devices, as well as GMail, Outlook, Apowersoft Phone Manager, and others, in Windows® . Supports vcard vcf 2.1, vcf 3.0, vcf 4.0, xcard 4.0, and jcard 4.0. Can run from a USB drive. Help file and example VCF, XML, and JSON files are provided too. -
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
...DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. DeepTrio is a deep learning-based trio variant caller built on top of DeepVariant. DeepTrio extends DeepVariant's functionality, allowing it to utilize the power of neural networks to predict genomic variants in trios or duos. See this page for more details and instructions on how to run DeepTrio. Out-of-the-box use for PCR-positive samples and low quality sequencing runs, and easy adjustments for different sequencing technologies and non-human species. -
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vcparse
A simplistic C++ VCF/VCARD parser
This single-file project transcodes VCF/VCARD files into JSON for easy filtering with grep. VCARD support is incomplete but can be extended. This project was motivated from recovering contacts backed up from an Android phone in a human-readable yet machine-friendly format. -
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VCF5
Federated Open Micro-formatting Project
Variant Calling File format version 5.0 this project consists of the *.vcf file format resources as well as definitions files and control files... This project allows for more than one contributor to change and modify data in appurtenance too the run-time and operations of the VCF version 5 file format. -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
...The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. A complete list of functionalities is available in our wiki (https://sourceforge.net/p/ngsep/wiki/Home/). ... -
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vcf2maf
Convert a VCF into a MAF
vcf2maf is a Perl-based tool developed by the Memorial Sloan Kettering Cancer Center to convert Variant Call Format (VCF) files into Mutation Annotation Format (MAF) files. This conversion standardizes variant annotations, facilitating downstream analyses in cancer genomics. -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. ... -
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SPiCEv2.1
Splicing Prediction in Consensus Element
...To access the tool's predictions, please use SPiP, accessible at : https://sourceforge.net/projects/splicing-prediction-pipeline/ or https://github.com/raphaelleman/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1.5 (05/2019) + corr (01/2020): Fix bug for linux version v2.1.4 (03/2019): Proxy management (only for Windows version) v2.1.3 (07/2018): correction bug for first 3' ss import vcf file v2.1.2 (06/2018): Import duplication Simplify import of deletion with one nucleotide Use tryCatch Improving web api connection check -
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A Simple VCF (Virtual Contact File) Viewer/Editor/Creator in JavaScript (VCF versions 2.1/3.0/4.0) What is a VCF file? A VCF file is a standard file format for storing contact information for one or more persons or a business. It typically includes a name, address, phone number, email address, and other contact information. VCF files also support custom fields, images, and other types of media.
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10
Free VCF file to CSV or Excel converter
Excel VBA Script to convert VCF file with multiple entries to CSV file
...If this doesn't work for you, please email me the VCF file and I'll modify the code to support your specific VCF format. To use, simply download and open the Excel file (xlsm), Enable Macros if prompted, and then select the VCF file you wish to import. Once complete, Excel will create and save new file titled VCFExport.csv that can also be saved in Excel format. -
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GnuAccounting
Cross-plattform java invoicing and accounting application
An open-source java accounting application that integrates OpenOffice, Apache Derby and HBCI/FinTS to create and manage invoices, credit memos, delivery notes, bills etc. Imports from kTimeTracker, Task Coach, VCF, Hibiscus, Moneyplex, Starmoney, exports to Winston, VCF, openTrans et. al. -
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AUDACITY
AUtozygosity iDentification And ClassIfication Tool
AUDACITY is novel computational approach 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. AUDACITY is a tool integrating novel RoH detection algorithm and autozygosity prediction score for prioritization of mutation-surrounding regions. ###################################################################### The AUDACITY tool has been published on Computational and Structural Biotechnology Journal (CSBJ). . ... -
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akcansoft XLS-to-VCF
This Excel file exports contact information from a table to a vcf file
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mod_psldap
Apache LDAP Directory Manager
mod_psldap is an Apache module for leveraging LDAP services built on the OpenLDAP library and the Apache APIs, to include web based A&A, web based updates to the LDAP store, server-side XSLT processing, and session management across servers. -
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...The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). HTDP provides quick filtering functionality and can process data consisting of single or multiple input files. Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. ...
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csv2vcf converter
csv(Comma-Separated Values) to vCard 2.1 converter
This software will help you to convert a .csv(Comma-Separated Values) files to .vcf(vCard 2.1) files. For example, you'll find it very helpful for transfering your contacts from old-types cell phones, wich can export it's phonebook to csv only, to newer ones or even smartphones, etc. The latest version from now on has the ability of language selection. The built in languages are: English, Ukrainian and Russian. -
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VCF Split
Vcard File Splitter
This little Java Program splits a VCF file consisting of multiple vcarss into single files. This is particualry useful if you want to import a vcf into Microsoft Outlook. It ist a executable jar file, so starting it with java -jar vcfsplitter.jar or double clicking it in a gui should work fine. You can also specify evertyhing by command line as follows: java -jar vcfsplitter.jar <infile> <outdir> For the source click on the website link.. -
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VCF Reader
A tool that enables users select and view contact details from a vCard
A tool that enables users select and view contact details from a vCard (.vcf) format. It also has search functionality and remembers your last viewed file. -
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testtd
Logiciel RegistreTPE
...Le logiciel permet d’importer et d’exporter des fichiers provenant de BaseProspect (fichier .bp) ainsi que des fichiers de contact provenant des smartphones (fichier .vcf) permettant ainsi la liaison entre le logiciel BaseProspect et les smartphones des commerçants de la société. De plus, il est possible de choisir les contacts à exporter et un système de mise à jour permet de consulter l’historique des modifications de contact. Enfin, le logiciel se présente sous forme d’une interface en ligne de commande qui permet d’accéder aux différentes fonctions proposées. -
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VCF Explorer
A desktop application for analyzing whole genome VCF files
VCF-Explorer can be run at different environments and computational platforms ranging from a standard laptop to an advanced server. -
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DaMold
a data mining platform for variant annotation and visualization.
DaMold a powerful, integrated, web-based, and user-friendly tool to filter, annotate, cross-link, and visualize NGS, Sanger, and hotspot variants. It is easy-to-use software, which provides flexible input options and accepts variants in VCF and BED formats. For each variant DaMold predicts the variant effect, such as codon change, and amino acid change. Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and INDELs from previous experimental studies along with associated genomic, proteomic, and clinical information. ... -
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csv2vcf in php
web based csv2vcf tool
convert csv2vcf csv2vcf,csv,vcf,android,addressbook,address,book http://dwaves.de/tools/csv2vcf/ -
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MIPVAR
MIP VARiant calling tool
...Run command: java -Dsnappy.disable=true -Dlogging.config=/path-to-pipeline/MIPVAR-<version>-package/conf/logback.xml -cp "/path-to-pipeline/MIPVAR-<version>-package/lib/*" org.umcn.gen.mip.pipeline.RunMIPPipeline -sampleConfig /path-to-file/sampleConfig.txt -environment EMPTY -overridePipelineConfig /path-to-file/runConfig.txt Output: - Bam files per sample - VCF - Coverages per MIP per Sample -
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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.
