Search Results for ".vcf file opener"
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Showing 42 open source projects for ".vcf file opener"
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Bright Data - All in One Platform for Proxies and Web ScrapingBright Data offers the highest quality proxies with automated session management, IP rotation, and advanced web unlocking technology. Enjoy reliable, fast performance with easy integration, a user-friendly dashboard, and enterprise-grade scaling. Powered by ethically-sourced residential IPs for seamless web scraping.
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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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nnn
The missing terminal file browser for X
nnn is a fork of noice, a blazing-fast lightweight terminal file browser with easy keyboard shortcuts for navigation, opening files and running tasks. noice is developed considering terminal based systems. There is no config file and mime associations are hard-coded. However, the incredible user-friendliness and speed make it a perfect candidate for modern distros. nnn works with the desktop opener, adds new navigation options, navigate-as-you-type mode, enhanced DE integration, bookmarks... -
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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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CliFM
The command line file manager
A file manager for the Unix terminal. Unlike most file managers out there, based on the TUI, CliFM is entirely based on command-line. It is also ultra-lightweight, lightning fast, extensible, and written in C. -
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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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Freeter
The smartest way to work on your computer
... tired of switching between accounts, the widget also enables you to stay signed-in with different accounts on per-project, per-workflow or per-widget basis. Use the file opener widget to open all project files and folders in your editing programs with a single click. Use the web query widget to quickly perform templated queries with a web search engine or any other website. Stop keeping checklists and to-do lists in your head. Let the to-do list widget remember them for you. And more... -
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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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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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Walnut
Open Advent Axys files without running Axys32.exe
** v2018.01.01 ** is here! Read about the improvements in the release notes in the Files section. Please report any issues to info@opulos.com Thanks! Walnut is for financial firms that want to open an alternative way to open files created in Advent Axys. Opulos offers a commercial product called NuWorkflow which loads Axys files into a SQL database. It also improves business operations for financial firms via automation and quality assurance checking. If you like Walnut then you will... -
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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... -
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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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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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VCF Explorer
A desktop application for analyzing whole genome VCF files
he decreasing cost high-throughput technologies led to a number of sequencing projects consisting thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyze exome files are not adequate for large VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Efficient memory management... -
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MIPVAR
MIP VARiant calling tool
... in the example input files (see sampleConfigExample.txt and runConfigExample.txt). 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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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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denovo_hit
Outputs potential denovo variants from VCF given pedigree information.
Program takes variants calls and determines if the call is novel for a child compared to parents. Program can handle both annotated and unannotated VCF files, however output file is not compatible with GATK's snpEff, so you should annotate prior to using denovo_hit. Usage: ./denovo_hit <VCF file> <PED file> Output: ./potential_denovo.txt To compile: g++ -std=c++11 denovo_hit.cpp -o denovo_hit Please see files for example VCF file, and pedigree file. Format VCF file (tab delimited... -
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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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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...
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
...-defining polymorphism. 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
... the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. 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... -
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snpSniffer
snpSniffer is a sample integrity checking tool for NGS data
-- About snpSniffer -- snpSniffer is a genotype based sample integrity checking tool for next generation sequencing 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...