Search Results for ".vcf file opener" - Page 2
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Showing 63 open source projects for ".vcf file opener"
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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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File Hider
File Hider used to hide files
The File Hider is used to hide files in windows. It uses super hide method of windows and it can open the files which is hidden by virus programs. -
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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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Split VCF
Split Contacts
Google Exports Contacts as Single File. But Where as Nokia and Microsoft Supports Single Files. I designed this Software as a solution to this Problem. For password mail Me to arjun143malli@gmail.com -
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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... -
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VCFSplitter
Splits combined VCF to individual VCF files
This software shall help you to split your single vcf file which has multiple vcf entries to individual VCF files. -
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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... -
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estMOI
estimating Multiplicity Of Infection using short read sequence data
estMOI is intended to estimate Multiplicity of Infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data as follows: INPUT files: estMOI requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. 1. Short reads are aligned to a reference genome using... -
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VCFannotator
Annotate SNPs in the context of Gene Annotations
A VCF file is parsed to identify genomic variations, and these variations are placed in the context of genome feature annotations. In the case that a mutation is coding, the type of coding mutation and impact on the protein-coding sequence is indicated. -
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VCard to XLS is a utility that I created to convert a VCard file with multiple entries into Microsoft Excel format. Once in Excel, the file can be saved as a Comma Separated Values file (.CSV) and imported into may different programs.
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rcard
ncurses VCard 3.0 contact management editor
A vcard 3.0 contact management editor developed for ncurses. It can: - load a vcf file - show all the contacts in a list - show more information about a single contact - perform a simple search in the contacts list - edit contacts - support UTF-8 (currently not on WIN32, though I'm not sure WIN32 console is actually able to support UTF-8) - convert the VCF(s) to Pine/Alpine addressbook format - import images from files as contacts photos The idea is based upon rolo (which you can... -
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PhonixJ
A cross-platform phone-book written in Java using SWT.
PhonixJ is a simple, light and feature rich desktop phone-book application written in Java. It uses Sqlite database files, so it is quite portable. The program runs on Linux, Windows and (soon coming ) MacOS. Features: - Add/remove contacts - Create vCard v.3.0 - Create Contact Card in .SVG - Create mail envelope address - Sophisticated search engine - Customizable printing options - Support for email and browser clients - Batch export/import of the contacts via .vcf (3.0) files... -
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QR Gen
Multi-platform QR code generator from information supplied
QRGen creates QR codes from contact information, written in Java. It requires the tool qrencode in order to work, qrencode is freely available at http://fukuchi.org/works/qrencode (Linux/Mac OS/UNIX) , or http://code.google.com/p/qrencode-win32/ (Windows), or Ubuntu Software Centre. -
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Excel to VCF converter
A free tool to convert Excel file to Vcard v2.1
... correctly please tweak the row numbers and the column names appropriately till the required data is properly read inside the tool. 4. Finally click on the create Vcf file , select the required folder. Vcf file will be created. a) Vcf file name is given accordingly "LAST NAME" "FIRST NAME".vcf b) Individual Vcf is created for individual contacts. This is in early stages of development for any bug report please post a comment in my blog. This is tested on Windows 7 with Office 2010 -
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vcf2csv
(abandoned and outdated project) convert vcard data into csv format
vcf2csv is a command line tool, written in ANSI-C (C90), converts a vcard (vcf) file to csv. Please note: the ability to generate HTML-files will be removed in the near future. -
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dbVcfSplitter - vCard Splitter
vCard file splitter
You can export Google contacts and import to your Nokia phones very easily. Just export the Google contacts in vCard format (.vcf file). Split the file using "dbVcfSplitter" and import those files using your Nokia PC Suite or OVI Suite. Done!! Usage: (1) Open the Command Prompt or the terminal. (2) "cd" to the folder/directory where the .vcf file resides. (3) type as shown below java -jar dbVcfSplitter.jar filename.vcf -
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Translate VCF
Determine functional consequences of mutations in a vcf file
Takes vcf file input and determines functional consequence of mutations with regard to UCSC known genes, refseq genes or ensembl genes. Will use UCSC known gene annotation by default. A correctly formatted CDS file must be used containing CDS sequences and gene table info (i.e. info from knownGene.txt for UCSC genes, refGene.txt for RefSeq or ensGene.txt for ensembl as downloaded from the UCSC downloads page [http://hgdownload.cse.ucsc.edu/downloads.html or ftp://hgdownload.cse.ucsc.edu... -
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abcontamination
Plots allele balance histogram and assesses sample contamination.
This software (plot_allele_balance_find_contamination.pl) produces an allele balance histogram and assesses DNA contamination of a single sample in a VCF file (vers. 3 & 4) that has been annotated in the info field for the AB=<num> metric in the range 0 - 1.0. It requires that the R statistical package is installed and in your path and can be run on the Linux, Unix or Mac computer. It does not work on multi-sample VCF files. If your VCF is not annotated for AB=<num> you may do this using...