Search Results for "vcf"
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Showing 86 open source projects for "vcf"
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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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Simple Contacts
Easy and quick contact management with no ads, handles groups
A lightweight smart contact app for managing your contacts loved by millions of people. The contacts can either be stored on your device only, or they can also be synchronized by different means. This phone number smart contact phone book will help you keep your contacts in one place without the hassle of backing up your contacts as the contacts backup are always in sync with the contacts you add. This app light on space and is effective when you have to make contacts backup and keep a phone... -
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 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... -
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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. Live demo at: https://virtual-contact-file-manager.sourceforge.io/ Features...
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Picsart Enterprise Background Removal API for Stunning eCommerce VisualsWith our Remove Background API tool, you can access the transformative capabilities of automation , which will allow you to turn any photo asset into compelling product imagery. With elevated visuals quality on your digital platforms, you can captivate your audience, and therefore achieve higher engagement and sales.
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vcard program vCardz_i
VCF vcard, XML xcard, JSON jcard;View, Edit, Convert, Export, CSV, QR
vCardz_i supports VCF, XML and JSON vcards; View, Create, Edit, Extract, Convert, Import CSV, TAB or |, Export CSV, Excel® .xlsx, TXT or ODS spreadsheet. Create vcard QR code images, in MEcard, vCard or xCard format., or create your own QR from your text entry. Voice output of selected data or a complete address. Create multiple Themes to easily switch appearance. Free multifunction vcard address book program to handle multilingual VCF, XML and JSON vcard files. Use the same vcards... -
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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. BMC... -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. 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... -
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crossmap
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format. -
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Multiuser HylaFAX PHP/MySQL Web interface for viewing faxes online, downloading & emailing in PDF format, and categorizing & archiving all sent and received faxes.
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Lung cancer screening panel
Software for predicting probability of lung cancer from VCF file
We have developed a lung cancer screening panel based on the occurrence of specific clonal hematopoietic mutations in peripheral blood samples. The software provided here can be used to predict the probability of cancer from peripheral blood samples. The sequencing data from the blood sample should be first aligned to the GRCh38 reference genome using the Burroughs-Wheeler aligner and variants called using the Mutect2 for variant calling. The resulting VCF file is used as input to the software... -
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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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SPiCEv2.1
Splicing Prediction in Consensus Element
SPiCE is no longer maintained. 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... -
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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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Free VCF file to CSV or Excel converter
Excel VBA Script to convert VCF file with multiple entries to CSV file
This is an Excel based VBA script used to import bulk .VCF files that contain more than 1 Vcard and then convert them to a comma separated .CSV file or Excel xls file that can then be imported into Outlook, Google, or any other application that supports import of contacts using CSV files. This has been written to support VCF 2.0, 2.1, 3.0 and 4.0 formatted files including those with printable encoding (MIME) and has been tested with bulk VCF files from Backupify, Google Contacts (Gmail... -
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filterSAMbyVCF
his program extracts reads from SAM file according to SNPs from a VCF
filterSAMbyVCF is a Pascal command line program to separate allele-specific reads from a SAM file. This program extracts reads from SAM file according to SNPs from VCF file. Extracted reads have ALT allele at the position given in VCF file. Usage with UNIX/Linux/MacOS: ./filterSAMbyVCF vcfFile.vcf samFile.sam Usage with Windows: filterSAMbyVCF.exe vcfFile.vcf samFile.sam No warranty of any kind is provided. Use at your own risk. -
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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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akcansoft XLS-to-VCF
This Excel file exports contact information from a table to a vcf file
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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... -
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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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variantkey
Binary files for variantkey
Binary files for the variantkey library: https://github.com/Genomicsplc/variantkey The binary files are generated using the script: https://github.com/Genomicsplc/variantkey/blob/master/resources/tools/vkhexbin.sh from the Human Variation Sets in VCF Format [National Library of Medicine (NLM)]: ftp://ftp.ncbi.nih.gov/snp/organisms/ -
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vCard-to-CSV
Makes vCard (.vcf) data readable
Makes vCard (.vcf) data readable Full security nothing is uploaded, everything just plays out their computer with the language JavaScript. Just download and double click on 'vCard-to-CSV.html' file! Tested with a contacts.vcf file from my Android Samsung smartphone. Runs on almost every device! Download: https://sourceforge.net/projects/vcard-to-csv/files/vCard-to-CSV.html/download - When it is helpful, please rate this project. - Newest version is 2.1 from 1... -
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vCard-Reader-viewer
Makes vCard (.vcf) data readable
Makes vCard (.vcf) data readable Full security nothing is uploaded, everything just plays out their computer with the language JavaScript. Just download and double click on 'vCard-to-CSV.html' file! Tested with a contacts.vcf file from my Android Samsung smartphone. Runs on almost every device! Download: https://sourceforge.net/projects/vcard-reader-viewer/files/vCard-Reader.html/download When the message: Software download arent't possible on this device. Then click klick bottom... -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. 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...
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by... -
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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. Besides, users can even make own translations now and store them into languages.ini...
