The European Variation Archive
|
|
|
- Opal Morgan
- 5 years ago
- Views:
Transcription
1 The European Variation Archive Webinar: A database of all types of genomic variation data from all species Hannah McLaren eva-helpdesk@ebi.ac.uk
2 Learning objectives Establish the key functions of the EVA resource Discover how to access variation data through the website and REST API Understand the submission process and data requirements Latest updates on the dbsnp import and generation of rs IDs for non-human species
3 Data resources at EMBL-EBI
4 European Variation Archive (EVA) Short Variants Variants: 750 million Studies: 351 Species: 46 Database of Genomic Variants archive Separate archive for more complex variation Human data shared with dbvar SVs downloadable from both EVA/DGVa websites Future plans to unify the two resources Structural Variants
5 Population data available at EVA
6 European Variation Archive (EVA) Variants SNVs, MNVs, indels & structural variants Germline or somatic Within/across population (including subspecies but not across species) Human variation for public access only Sample genotypes Study Metadata Experiment/Analyses Samples Accessions Annotation Effect on genes/transcripts Functional consequence Population frequencies
7 User experience VCF Download Browse CSV Submit
8 Study Browser
9 Study View
10 Study Browser Structural Variants Sourced from Database of Genomic Variants archive (DGVa) which is shared with dbvar at NCBI
11 Study View Structural Variants
12 Variant Browser RS ID - uniquely identifies a variant Filter By: Gene Symbol/Accession - ex: BRCA2 Variant ID (rsid or ssid) ex: rs Chromosomal location ex: 13: Source Studies, Consequence type, MAF, Protein substitution score
13 Variant Browser
14 Clinical Assertions
15 Variant Browser
16 Variant Browser
17 Variant Browser
18 REST API Programmatic access through web services API Variant Browser uses this API Results provided in JSON Easily parsed by Python, R, Java Web services for Files, segments, studies, variants, genes Full documentation at EVA website
19 REST API - Example Use the gene name BRCA2 as an endpoint Species representation Homo Sapiens with the grch37 reference assembly Page offset and number of results to fetch Sequence Ontology (SO) accession for Frameshift Mutations
20 Why EVA? Open access population data Permanent archive, traceability of data Stable accessions Data validated, normalized and annotated via Variant Effect Predictor (VEP) Dynamic search through the Variant Browser and programmatic access through the REST API Data sharing standards (GA4GH)
21 User experience - Submission VCF Download Browse CSV Submit
22 Submission - Data requirements 1. Data is described in valid VCF file(s) Data includes sample genotypes and/or allele frequencies 3. The reference sequence used is INSDC registered Variant accessions (ss# and rs#) and study accessions will only be provided for data which satisfies these data requirements.
23 Variant Call Format (VCF) Specification can be found at:
24 Variant accessioning New subsnp ID (ss#) after successful submission Human Non-human New Reference SNP IDs (rs#) after periodic clustering o First rs# release predicted 2018 Q4 o No rs# for Structural Variants Existing ss#/rs# from dbsnp will be maintained
25 dbsnp import All non-human variants by species Variants browsable if they satisfy all EVA submission requirements Human Non-human Import progress at -Import-Progress
26 EVA summary Open access, submission-based resource All variants, all species Data brokered to other resources at EMBL-EBI (ENA, BioSamples, DGVa) NCBI (dbsnp, dbvar) Stable accessions for publication Submissions can be held until publication rsid accessioning for non-human (dbsnp for human) Import of existing dbsnp data in progress Download FTP/API
27 Announcements Mailing list: Feedback Feature requests and bug reports: Website: REST API:
28 Acknowledgments EVA / DGVA Thomas Keane Cristina Yenyxe González Pablo Arce Andres Silva Jose Miguel Mut Sundar Venkataraman Hannah McLaren Baron Koylass EGA Dylan Spalding Jag Kandasamy Giselle Kerry Jorge Izquierdo Ciges ENA Rasko Leinonen Marc Rosello Ensembl Variation Fiona Cunningham Sarah Hunt Anja Thormann Laurent Gil Helen Schuilenberg
BaseSpace Variant Interpreter Release Notes
Document ID: EHAD_RN_010220118_0 Release Notes External v.2.4.1 (KN:v1.2.24) Release Date: Page 1 of 7 BaseSpace Variant Interpreter Release Notes BaseSpace Variant Interpreter v2.4.1 FOR RESEARCH USE
SNP/SNV effect and annotation
SNP/SNV effect and annotation Laurent Falquet, Oct 18 Why annotating the SNVs? Annotate the function of a mutation (change or the effect of a variant) Restrict the space of search Ultimate goal: allow
Click on "+" button Select your VCF data files (see #Input Formats->1 above) Remove file from files list:
CircosVCF: CircosVCF is a web based visualization tool of genome-wide variant data described in VCF files using circos plots. The provided visualization capabilities, gives a broad overview of the genomic
Automating the Collection and Processing of Cancer Mutation Data
Automating the Collection and Processing of Cancer Mutation Data Master s Project Report Jeremy Watson Advisor: Ben Raphael 1. Introduction 1 The Raphael lab has developed multiple software packages, such
PriVar documentation
PriVar documentation PriVar is a cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from exome or whole genome sequencing data by using different filtering strategies and
NGS Data Analysis. Roberto Preste
NGS Data Analysis Roberto Preste 1 Useful info http://bit.ly/2r1y2dr Contacts: roberto.preste@gmail.com Slides: http://bit.ly/ngs-data 2 NGS data analysis Overview 3 NGS Data Analysis: the basic idea http://bit.ly/2r1y2dr
ClinVar. Jennifer Lee, PhD, NCBI/NLM/NIH ClinVar
ClinVar What is ClinVar ClinVar is a freely available, central archive for associating observed variation with supporting clinical and experimental evidence for a wide range of disorders. The database
myvcf Documentation Release latest
myvcf Documentation Release latest Oct 09, 2017 Contents 1 Want to try myvcf? 3 2 Documentation contents 5 2.1 How to install myvcf.......................................... 5 2.2 Setup the application...........................................
Enabling Open Science: Data Discoverability, Access and Use. Jo McEntyre Head of Literature Services
Enabling Open Science: Data Discoverability, Access and Use Jo McEntyre Head of Literature Services www.ebi.ac.uk About EMBL-EBI Part of the European Molecular Biology Laboratory International, non-profit
CircosVCF workshop, TAU, 9/11/2017
CircosVCF exercise In this exercise, we will create and design circos plots using CircosVCF. We will use vcf files of a published case "X-linked elliptocytosis with impaired growth is related to mutated
Analyzing Variant Call results using EuPathDB Galaxy, Part II
Analyzing Variant Call results using EuPathDB Galaxy, Part II In this exercise, we will work in groups to examine the results from the SNP analysis workflow that we started yesterday. The first step is
User Guide. v Released June Advaita Corporation 2016
User Guide v. 0.9 Released June 2016 Copyright Advaita Corporation 2016 Page 2 Table of Contents Table of Contents... 2 Background and Introduction... 4 Variant Calling Pipeline... 4 Annotation Information
Practical exercises Day 2. Variant Calling
Practical exercises Day 2 Variant Calling Samtools mpileup Variant calling with samtools mpileup + bcftools Variant calling with HaplotypeCaller (GATK Best Practices) Genotype GVCFs Hard Filtering Variant
The software comes with 2 installers: (1) SureCall installer (2) GenAligners (contains BWA, BWA- MEM).
Release Notes Agilent SureCall 4.0 Product Number G4980AA SureCall Client 6-month named license supports installation of one client and server (to host the SureCall database) on one machine. For additional
Updated for release (July 2015) 1.4 User Manual
Updated for release 1.4.2 (July 2015) 1.4 User Manual This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the contractual use of its customer in connection
WheatIS: Progress report
WheatIS: Progress report WheatIS Annual meeting, San Diego, 9 January 2015 WheatIS data submission DSpace Beta-version to test: http://urgi.versailles.inra.fr/xmlui/ At the moment, available submission
Alamut Focus 0.9 User Guide
0.9 User Guide Alamut Focus 0.9 User Guide 1 June 2015 Alamut Focus 0.9 User Guide This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the contractual
Introduction to Genome Browsers
Introduction to Genome Browsers Rolando Garcia-Milian, MLS, AHIP (Rolando.milian@ufl.edu) Department of Biomedical and Health Information Services Health Sciences Center Libraries, University of Florida
Genome Browsers Guide
Genome Browsers Guide Take a Class This guide supports the Galter Library class called Genome Browsers. See our Classes schedule for the next available offering. If this class is not on our upcoming schedule,
EBI services. Jennifer McDowall EMBL-EBI
EBI services Jennifer McDowall EMBL-EBI The SLING project is funded by the European Commission within Research Infrastructures of the FP7 Capacities Specific Programme, grant agreement number 226073 (Integrating
Alamut Batch 1.4 User Manual
1.4 User Manual This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the contractual use of its customer in connection with the use of the product(s)
SAVANT v1.1.0 documentation CONTENTS
SAVANT v1.1.0 documentation CONTENTS 1 INTRODUCTION --------------2 2 INSTALLATION --------------2 3 RUNNING SAVANT ------------3 4 CONFIGURATION FILE --------4 5 INPUT FILE ----------------5 6 REFERENCE
Intro to NGS Tutorial
Intro to NGS Tutorial Release 8.6.0 Golden Helix, Inc. October 31, 2016 Contents 1. Overview 2 2. Import Variants and Quality Fields 3 3. Quality Filters 10 Generate Alternate Read Ratio.........................................
BaseSpace Variant Interpreter Release Notes
v.2.5.0 (KN:1.3.63) Page 1 of 5 BaseSpace Variant Interpreter Release Notes BaseSpace Variant Interpreter v2.5.0 FOR RESEARCH USE ONLY 2018 Illumina, Inc. All rights reserved. Illumina, BaseSpace, and
Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING)
Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) Reporting guideline statement for HLA and KIR genotyping data generated via Next Generation Sequencing (NGS) technologies and analysis
Updated for release (July 2016) 1.5 User Manual
Updated for release 1.5.2 (July 2016) 1.5 User Manual This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the contractual use of its customer in connection
MIRING: Minimum Information for Reporting Immunogenomic NGS Genotyping. Data Standards Hackathon for NGS HACKATHON 1.0 Bethesda, MD September
MIRING: Minimum Information for Reporting Immunogenomic NGS Genotyping Data Standards Hackathon for NGS HACKATHON 1.0 Bethesda, MD September 27 2014 Static Dynamic Static Minimum Information for Reporting
HymenopteraMine Documentation
HymenopteraMine Documentation Release 1.0 Aditi Tayal, Deepak Unni, Colin Diesh, Chris Elsik, Darren Hagen Apr 06, 2017 Contents 1 Welcome to HymenopteraMine 3 1.1 Overview of HymenopteraMine.....................................
Genomics. Nolan C. Kane
Genomics Nolan C. Kane Nolan.Kane@Colorado.edu Course info http://nkane.weebly.com/genomics.html Emails let me know if you are not getting them! Email me at nolan.kane@colorado.edu Office hours by appointment
The software comes with 2 installers: (1) SureCall installer (2) GenAligners (contains BWA, BWA-MEM).
Release Notes Agilent SureCall 3.5 Product Number G4980AA SureCall Client 6-month named license supports installation of one client and server (to host the SureCall database) on one machine. For additional
Maximizing Public Data Sources for Sequencing and GWAS
Maximizing Public Data Sources for Sequencing and GWAS February 4, 2014 G Bryce Christensen Director of Services Questions during the presentation Use the Questions pane in your GoToWebinar window Agenda
ELIXIR Human Data Use Case
ELIXIR Human Data Use Case Mikael Borg, ELIXIR Sweden ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.
UCSC Genome Browser ASHG 2014 Workshop
UCSC Genome Browser ASHG 2014 Workshop We will be using human assembly hg19. Some steps may seem a bit cryptic or truncated. That is by design, so you will think about things as you go. In this document,
Network Based Models For Analysis of SNPs Yalta Opt
Outline Network Based Models For Analysis of Yalta Optimization Conference 2010 Network Science Zeynep Ertem*, Sergiy Butenko*, Clare Gill** *Department of Industrial and Systems Engineering, **Department
4.1. Access the internet and log on to the UCSC Genome Bioinformatics Web Page (Figure 1-
1. PURPOSE To provide instructions for finding rs Numbers (SNP database ID numbers) and increasing sequence length by utilizing the UCSC Genome Bioinformatics Database. 2. MATERIALS 2.1. Sequence Information
Creating and Using Genome Assemblies Tutorial
Creating and Using Genome Assemblies Tutorial Release 8.1 Golden Helix, Inc. March 18, 2014 Contents 1. Create a Genome Assembly for Danio rerio 2 2. Building Annotation Sources 5 A. Creating a Reference
Applications of a generic model of genomic variations functional analysis
Applications of a generic model of genomic variations functional analysis Sarah N. Mapelli, Uberto Pozzoli data annotations variations FUNCTION The tools developer point of view: a general analysis flow
Demo 1: Free text search of ENCODE data
Demo 1: Free text search of ENCODE data 1. Go to h(ps://www.encodeproject.org 2. Enter skin into the search box on the upper right hand corner 3. All matches on the website will be shown 4. Select Experiments
Genome Assembly Using de Bruijn Graphs. Biostatistics 666
Genome Assembly Using de Bruijn Graphs Biostatistics 666 Previously: Reference Based Analyses Individual short reads are aligned to reference Genotypes generated by examining reads overlapping each position
Database of Curated Mutations (DoCM) ournal/v13/n10/full/nmeth.4000.
Database of Curated Mutations (DoCM) http://docm.genome.wustl.edu/ http://www.nature.com/nmeth/j ournal/v13/n10/full/nmeth.4000.h tml Home Page Information in DoCM DoCM uses many data sources to compile
Mutalyzer webservices. Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics
Mutalyzer webservices Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Introduction Mutalyzer: a curational tool for Locus Specific
Package ensemblvep. April 5, 2014
Package ensemblvep April 5, 2014 Version 1.2.2 Title R Interface to Ensembl Variant Effect Predictor Author Valerie Obenchain , Maintainer Valerie Obenchain Depends
Assignment 7: Single-cell genomics. Bio /02/2018
Assignment 7: Single-cell genomics Bio5488 03/02/2018 Assignment 7: Single-cell genomics Input Genotypes called from several exome-sequencing datasets derived from either bulk or small pools of cells (VCF
Oracle Health Sciences Omics Data Bank
Oracle Health Sciences Omics Data Bank Programmer s Guide Release 3.0.2.1 E35680-12 March 2016 Oracle Health Sciences Omics Data Bank Programmer s Guide Release 3.0.2.1 E35680-12 Copyright 2013, 2016,
Reference & Track Manager
Reference & Track Manager U SoftGenetics, LLC 100 Oakwood Avenue, Suite 350, State College, PA 16803 USA * info@softgenetics.com www.softgenetics.com 888-791-1270 2016 Registered Trademarks are property
CLC Server. End User USER MANUAL
CLC Server End User USER MANUAL Manual for CLC Server 10.0.1 Windows, macos and Linux March 8, 2018 This software is for research purposes only. QIAGEN Aarhus Silkeborgvej 2 Prismet DK-8000 Aarhus C Denmark
Tutorial: Resequencing Analysis using Tracks
: Resequencing Analysis using Tracks September 20, 2013 CLC bio Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 Fax: +45 86 20 12 22 www.clcbio.com support@clcbio.com : Resequencing
Finding and Exporting Data. BioMart
September 2017 Finding and Exporting Data Not sure what tool to use to find and export data? BioMart is used to retrieve data for complex queries, involving a few or many genes or even complete genomes.
MiSeq Reporter Software Reference Guide for IVD Assays
MiSeq Reporter Software Reference Guide for IVD Assays FOR IN VITRO DIAGNOSTIC USE ILLUMINA PROPRIETARY Document # 15038356 Rev. 02 September 2017 This document and its contents are proprietary to Illumina,
BovineMine Documentation
BovineMine Documentation Release 1.0 Deepak Unni, Aditi Tayal, Colin Diesh, Christine Elsik, Darren Hag Oct 06, 2017 Contents 1 Tutorial 3 1.1 Overview.................................................
Performing whole genome SNP analysis with mapping performed locally
BioNumerics Tutorial: Performing whole genome SNP analysis with mapping performed locally 1 Introduction 1.1 An introduction to whole genome SNP analysis A Single Nucleotide Polymorphism (SNP) is a variation
Genomic Analysis with Genome Browsers.
Genomic Analysis with Genome Browsers http://barc.wi.mit.edu/hot_topics/ 1 Outline Genome browsers overview UCSC Genome Browser Navigating: View your list of regions in the browser Available tracks (eg.
CDIS Biomedical Data Commons
CDIS Biomedical Data Commons Computational Life Science Seminar Series October 18, 2017 Michael Fitzsimons Center for Data Intensive Science Agenda What is a Data Commons? Data Commons at CDIS NCI GDC
Alamut Focus User Manual
1.1.1 User Manual Alamut Focus 1.1.1 User Manual 1 5 July 2016 Alamut Focus 1.1.1 User Manual This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the
How to store and visualize RNA-seq data
How to store and visualize RNA-seq data Gabriella Rustici Functional Genomics Group gabry@ebi.ac.uk EBI is an Outstation of the European Molecular Biology Laboratory. Talk summary How do we archive RNA-seq
SNP Calling. Tuesday 4/21/15
SNP Calling Tuesday 4/21/15 Why Call SNPs? map mutations, ex: EMS, natural variation, introgressions associate with changes in expression develop markers for whole genome QTL analysis/ GWAS access diversity
Allele Registry. versions 1.01.xx. API specification. Table of Contents. document version 1
Allele Registry versions 1.01.xx API specification document version 1 Table of Contents Introduction...3 Sending HTTP requests...3 Bash...3 Ruby...4 Python...5 Authentication...5 Error responses...6 Parameter
Designing Custom GoldenGate Genotyping Assays
Designing Custom GoldenGate Genotyping Assays Guidelines for efficiently creating and ordering high-quality custom GoldenGate Genotyping Assays using the Illumina Assay Design Tool. Introduction The Illumina
Taking a view on bio-ontologies. Simon Jupp Functional Genomics Production Team ICBO, 2012 Graz, Austria
Taking a view on bio-ontologies Simon Jupp Functional Genomics Production Team ICBO, 2012 Graz, Austria Who we are European Bioinformatics Institute one of world s largest bio data and service providers
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords [version 1; referees: awaiting peer review]
![Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords [version 1; referees: awaiting peer review]](/thumbs/88/117074068.jpg "Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords [version 1; referees: awaiting peer review]")
SOFTWARE TOOL ARTICLE Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords [version 1; referees: awaiting peer review] Tamer Gur European Bioinformatics Institute,
Infinium iselect Custom Genotyping Assays Guidelines for using the DesignStudio Microarray Assay Designer software to create and order custom arrays.
Infinium iselect Custom Genotyping Assays Guidelines for using the DesignStudio Microarray Assay Designer software to create and order custom arrays. Introduction The Illumina Infinium Assay enables highly
Alamut Focus User Manual
1.2.0 User Manual Alamut Focus 1.2.0 User Manual 1 10 May 2017 Alamut Focus 1.2.0 User Manual This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the
When we search a nucleic acid databases, there is no need for you to carry out your own six frame translation. Mascot always performs a 6 frame
1 When we search a nucleic acid databases, there is no need for you to carry out your own six frame translation. Mascot always performs a 6 frame translation on the fly. That is, 3 reading frames from
1. Introduction. 2. System requirements
Table of Contents 1. Introduction...2 2. System requirements...2 3. Installation...3 4. Running on exemplary datasets...3 5. Preparing your own data to run Oncodrive-fm...4 1. Introduction Oncodrive-fm
1.8 USER MANUAL.
1.8 USER MANUAL www.interactive-biosoftware.com 12-10-2017 This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the contractual use of its customer in
User Manual. Ver. 3.0 March 19, 2012
User Manual Ver. 3.0 March 19, 2012 Table of Contents 1. Introduction... 2 1.1 Rationale... 2 1.2 Software Work-Flow... 3 1.3 New in GenomeGems 3.0... 4 2. Software Description... 5 2.1 Key Features...
ADNI Sequencing Working Group. Robert C. Green, MD, MPH Andrew J. Saykin, PsyD Arthur Toga, PhD
ADNI Sequencing Working Group Robert C. Green, MD, MPH Andrew J. Saykin, PsyD Arthur Toga, PhD Why sequencing? V V V V V V V V V V V V V A fortuitous relationship TIME s Best Invention of 2008 The initial
2. Take a few minutes to look around the site. The goal is to familiarize yourself with a few key components of the NCBI.
2 Navigating the NCBI Instructions Aim: To become familiar with the resources available at the National Center for Bioinformatics (NCBI) and the search engine Entrez. Instructions: Write the answers to
User s Guide Release 3.3
[1]Oracle Healthcare Translational Research User s Guide Release 3.3 E91297-01 October 2018 Oracle Healthcare Translational Research User's Guide, Release 3.3 E91297-01 Copyright 2012, 2018, Oracle and/or
Deliverable D4.3 Release of pilot version of data warehouse
Deliverable D4.3 Release of pilot version of data warehouse Date: 10.05.17 HORIZON 2020 - INFRADEV Implementation and operation of cross-cutting services and solutions for clusters of ESFRI Grant Agreement
Supplementary Note-- Williams et al The Image Data Resource: A Bioimage Data Integration and Publication Platform
Supplementary Note-- Williams et al The Image Data Resource: A Bioimage Data Integration and Publication Platform 1. Exploring the IDR This current IDR web user interface (WUI) is based on the open source
The ELIXIR of Linked Data
The ELIXIR of Linked Data Professor Carole Goble (UK node) Barend Mons (NL node), Helen Parkinson (EMBL-EBI node) The Interoperability Services Backbone Team European Life Sciences Infrastructure for Biological
BioMart: a research data management tool for the biomedical sciences
Yale University From the SelectedWorks of Rolando Garcia-Milian 2014 BioMart: a research data management tool for the biomedical sciences Rolando Garcia-Milian, Yale University Available at: https://works.bepress.com/rolando_garciamilian/2/
Alamut Focus 1.4 User Manual
1.4 User Manual Alamut Focus 1.4 User Manual This document and its contents are proprietary to Interactive Biosoftware. They are intended solely for the contractual use of its customer in connection with
Package ensemblvep. January 19, 2018
Package ensemblvep January 19, 2018 Version 1.20.0 Title R Interface to Ensembl Variant Effect Predictor Author Valerie Obenchain and Lori Shepherd Maintainer Bioconductor Package Maintainer
Data Walkthrough: Background
Data Walkthrough: Background File Types FASTA Files FASTA files are text-based representations of genetic information. They can contain nucleotide or amino acid sequences. For this activity, students will
Axiom Analysis Suite Release Notes (For research use only. Not for use in diagnostic procedures.)
Axiom Analysis Suite 4.0.1 Release Notes (For research use only. Not for use in diagnostic procedures.) Axiom Analysis Suite 4.0.1 includes the following changes/updates: 1. For library packages that support
Importing Next Generation Sequencing Data in LOVD 3.0
Importing Next Generation Sequencing Data in LOVD 3.0 J. Hoogenboom April 17 th, 2012 Abstract Genetic variations that are discovered in mutation screenings can be stored in Locus Specific Databases (LSDBs).
CAVA v1.2.0 documentation
CAVA v1.2.0 documentation CONTENTS 1 INTRODUCTION --------------------2 2 INSTALLATION --------------------2 3 RUNNING CAVA --------------------2 4 CONFIGURATION FILE --------------3 5 INPUT FILE ----------------------5
Human Disease Models Tutorial
Mouse Genome Informatics www.informatics.jax.org The fundamental mission of the Mouse Genome Informatics resource is to facilitate the use of mouse as a model system for understanding human biology and
epigenomegateway.wustl.edu
Everything can be found at epigenomegateway.wustl.edu REFERENCES 1. Zhou X, et al., Nature Methods 8, 989-990 (2011) 2. Zhou X & Wang T, Current Protocols in Bioinformatics Unit 10.10 (2012) 3. Zhou X,
Designing Custom GoldenGate Genotyping Assays
Designing Custom GoldenGate Genotyping Assays Guidelines for efficiently creating and ordering high-quality custom GoldenGate Genotyping Assays using the Illumina Assay Design Tool. Introduction The Illumina
Galaxy, 1000 Genomes and the GATK User Guide Page 1 of 18. Galaxy, 1000 Genomes and the GATK. Overview
Galaxy, 1000 Genomes and the GATK User Guide Page 1 of 18 Galaxy, 1000 Genomes and the GATK Overview Galaxy, 1000 Genomes and the GATK User Guide Page 2 of 18 Table of Contents 1) Introduction 2) Installation
TCGA Variant Call Format (VCF) 1.0 Specification
TCGA Variant Call Format (VCF) 1.0 Specification Document Information Specification for TCGA Variant Call Format (VCF) Version 1.0 1 About TCGA VCF specification 2 TCGA-specific customizations 3 File format
Variant Calling and Filtering for SNPs
Practical Introduction Variant Calling and Filtering for SNPs May 19, 2015 Mary Kate Wing Hyun Min Kang Goals of This Session Learn basics of Variant Call Format (VCF) Aligned sequences -> filtered snp
pvac-seq Documentation Release
pvac-seq Documentation Release 4.0.10 Jasreet Hundal, Susanna Kiwala, Aaron Graubert, Jason Walker, C Jan 16, 2018 Contents 1 Features 3 2 Installation 5 2.1 Installing IEDB binding prediction tools (strongly
Exome sequencing. Jong Kyoung Kim
Exome sequencing Jong Kyoung Kim Genome Analysis Toolkit The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic
Facilitating Semantic Alignment of EBI Resources
Facilitating Semantic Alignment of EBI Resources 17 th March, 2017 Tony Burdett Technical Co-ordinator Samples, Phenotypes and Ontologies Team www.ebi.ac.uk What is EMBL-EBI? Europe s home for biological
User's Guide to DNASTAR SeqMan NGen For Windows, Macintosh and Linux
User's Guide to DNASTAR SeqMan NGen 12.0 For Windows, Macintosh and Linux DNASTAR, Inc. 2014 Contents SeqMan NGen Overview...7 Wizard Navigation...8 Non-English Keyboards...8 Before You Begin...9 The
Ion AmpliSeq Designer: Getting Started
Ion AmpliSeq Designer: Getting Started USER GUIDE Publication Number MAN0010907 Revision F.0 For Research Use Only. Not for use in diagnostic procedures. Manufacturer: Life Technologies Corporation Carlsbad,
Welcome - webinar instructions
Welcome - webinar instructions GoToTraining works best in Chrome or IE avoid Firefox due to audio issues with Macs To access the full features of GoToTraining, use the desktop version by clicking switch
Gene Variant Databases & Sharing Information. Martina Witsch-Baumgartner Innsbruck, Austria
Gene Variant Databases & Sharing Information Martina Witsch-Baumgartner Innsbruck, Austria Diverse Genetic databases Aim of Gene Variant Databases Diagnostic databases Quality of Databases Sharing Data
Genome Browsers - The UCSC Genome Browser
Genome Browsers - The UCSC Genome Browser Background The UCSC Genome Browser is a well-curated site that provides users with a view of gene or sequence information in genomic context for a specific species,
KGG: A systematic biological Knowledge-based mining system for Genomewide Genetic studies (Version 3.5) User Manual. Miao-Xin Li, Jiang Li
KGG: A systematic biological Knowledge-based mining system for Genomewide Genetic studies (Version 3.5) User Manual Miao-Xin Li, Jiang Li Department of Psychiatry Centre for Genomic Sciences Department
Part 1: How to use IGV to visualize variants
Using IGV to identify true somatic variants from the false variants http://www.broadinstitute.org/igv A FAQ, sample files and a user guide are available on IGV website If you use IGV in your publication:
Mapping NGS reads for genomics studies
Mapping NGS reads for genomics studies Valencia, 28-30 Sep 2015 BIER Alejandro Alemán aaleman@cipf.es Genomics Data Analysis CIBERER Where are we? Fastq Sequence preprocessing Fastq Alignment BAM Visualization
Package seqcat. March 25, 2019
Package seqcat March 25, 2019 Title High Throughput Sequencing Cell Authentication Toolkit Version 1.4.1 The seqcat package uses variant calling data (in the form of VCF files) from high throughput sequencing
Topics of the talk. Biodatabases. Data types. Some sequence terminology...
Topics of the talk Biodatabases Jarno Tuimala / Eija Korpelainen CSC What data are stored in biological databases? What constitutes a good database? Nucleic acid sequence databases Amino acid sequence
BioBin User Guide Current version: BioBin 2.3
BioBin User Guide Current version: BioBin 2.3 Last modified: April 2017 Ritchie Lab Geisinger Health System URL: http://www.ritchielab.com/software/biobin-download Email: software@ritchielab.psu.edu 1
Decrypting your genome data privately in the cloud
Decrypting your genome data privately in the cloud Marc Sitges Data Manager@Made of Genes @madeofgenes The Human Genome 3.200 M (x2) Base pairs (bp) ~20.000 genes (~30%) (Exons ~1%) The Human Genome Project