Search Results for ".vcf"
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Showing 44 open source projects for ".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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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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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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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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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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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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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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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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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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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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The Visual Component Framework is intended as a cross platform class library, that supports, among other things, an advanced GUI framework strongly influenced by Borland's Visual Component Library and Java's Swing framework.
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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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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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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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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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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). ...
