Search Results for "vcf"
Sort By:
Showing 86 open source projects for "vcf"
View related business solutions-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
Project Planning and Management Software | PlanviewPlanview® ProjectAdvantage (formerly Sciforma) is an enterprise-centric project and portfolio management (PPM) software designed to enable change, drive innovation, and lead in a company's digital transformation. With ProjectAdvantage, teams can strategically track and monitor project data in order to make relevant decisions. It offers multiple features focused on strategic management, functional management, and execution management. A highly scalable and cost-effective solution, ProjectAdvantage is available in various deployment models.
-
1
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. -
2
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.">
-
3
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. -
4
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. -
Effortlessly Manage Product InformationA single source of truth for all of your product information with easy ways to distribute that data to wherever it needs to go, including the most powerful e-commerce connectors in the industry.
-
5
Lung cancer screening panel
Software for predicting probability of lung cancer from VCF file
...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. Output: Predicted probability of cancer. -
6
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. -
7
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/). ... -
8
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. ... -
9
Multiuser HylaFAX PHP/MySQL Web interface for viewing faxes online, downloading & emailing in PDF format, and categorizing & archiving all sent and received faxes.
-
Our xDM platform turns business users into data champions.It empowers organizations of any size to build trusted data applications quickly, with fast time to value using a single software platform for governance, master data, reference data, data quality, enrichment, and workflows.
-
10
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. -
11
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 -
12
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... -
13
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.
-
14
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. -
15
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. -
16
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. -
17
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). . ... -
18
akcansoft XLS-to-VCF
This Excel file exports contact information from a table to a vcf file
-
19
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. -
20
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 -
21
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. -
22
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/ -
23
...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. ...
-
24
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. -
25
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...