Title: Genome Variant Analysis Course 2014  
Author: Jeffrey E Barrick May 13, 2014
Last Changed by: Daniel Edward Deatherage May 22, 2014
Tiny Link: (useful for email) https://wikis.utexas.edu/x/qrv5Aw
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Incoming Links
Bioinformatics Team (BioITeam) at the University of Texas (5)
    Page: Genome Variant Analysis Course 2015
    Page: Read Mapping with bowtie2 Tutorial
    Page: Genome Variant Analysis Course 2016
    Page: Mapping with bowtie2 Tutorial
    Page: Mapping tutorial (bowtie2, bwa) (GVA14)
Hierarchy
Parent Page
    Page: Bioinformatics Courses and Content
Children (23)
    Page: Additional Useful Links (GVA14)
    Page: Advanced variant calling tutorial (GVA14)
    Page: An introduction to GATK (GVA14)
    Page: Annotating variants with annovar (GVA14)
    Page: Comparison of mixed population sequencing options (GVA14)
    Page: Evaluating and processing raw sequencing data (GVA14)
    Page: Exome capture metrics (GVA14)
    Page: Filtering and Screening Variants (GVA14)
    Page: General introduction to Genome Variant Analysis (GVA14)
    Page: Human Trios (GVA14)
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Recent Changes
Time Editor  
May 22, 2014 08:19 Daniel Edward Deatherage View Changes
Migrated to Confluence 5.3
May 22, 2014 08:19 Daniel Edward Deatherage View Changes
May 22, 2014 08:16 Daniel Edward Deatherage View Changes
May 22, 2014 08:13 Daniel Edward Deatherage View Changes
May 21, 2014 20:03 Daniel Edward Deatherage  
Outgoing Links
External Links (7)
    https://academy.nescent.org/wg/academy/images/0/0f/Variant_…
    barricklab.org
    https://wikis.utexas.edu/display/GSAF/Illumina+-+all+flavor…
    evomics.org/wp-content/uploads/2013/03/cesky_2014_RAD_tutor…
    https://wikis.utexas.edu/display/GSAF/About+Us#Scott
    https://etherpad.mozilla.org/V1EIko9FS5
    www.utexas.edu/maps/main/buildings/rlm.html
Bioinformatics Team (BioITeam) at the University of Texas (44)     Page: Mapped read data evaluation (samstat, SAMtools) (GVA14)
    Page: Step 1: Connecting to and establishing a profile on Lonestar (GVA14)
    Page: Genome Assembly (velvet)
    Page: Genome variation in mixed samples (FreeBayes, deepSNV)
    Page: Scott's list of linux one-liners
    Page: NGS Course Resources
    Page: SSCS vs Trimmed Read Variant calls (GVA14)
    Page: Example BWA alignment script
    Page: Comparison of mixed population sequencing options (GVA14)
    Page: Linux final
    Page: Genome Variant Analysis Course 2014
    Page: Installing Linux tools
    Page: Submitting a simple job using launcher_creator.py (GVA14)
    Page: Installing Virtual machine & Linux on Windows
    Page: Shell Script
    Page: Overview whole genome and complexity reduction methods (GVA14)
    Page: Exome capture metrics (GVA14)
    Page: Exercises
    Page: Visualize mapped data at UCSC genome browser
    Page: Evaluating & Visualizing assemblies
    Page: SV calling tutorial (GVA14)
    Page: Integrative Genomics Viewer (IGV) tutorial (GVA14)
    Page: Variant calling with GATK
    Page: Editing files
    Page: SRA toolkit
    Page: Samtools mpileup (GVA14)
    Page: General introduction to Genome Variant Analysis (GVA14)
    Page: Diagram of running a job on Lonestar
    Page: Identification of Variants in Mixed Population Sequencing (GVA14)
    Page: Annotating variants with annovar (GVA14)
    Page: Custom Genome Databases
    Page: Advanced variant calling tutorial (GVA14)
    Page: Using TACC's Lonestar cluster (GVA14)
    Page: Human Trios (GVA14)
    Page: SNV calling tutorial (GVA14)
    Page: Additional Useful Links (GVA14)
    Page: SSCS Read Generation (GVA14)
    Page: Genome Assembly
    Page: Evaluating and processing raw sequencing data (GVA14)
    Page: Mapping tutorial (bowtie2, bwa) (GVA14)
    Page: Filtering and Screening Variants (GVA14)
    Page: An introduction to GATK (GVA14)
    Page: SSC Intro to NGS Bioinformatics Course
    Page: Diagram of Lonestar's directories