Before we do anything else...
Log in to Lonestar, go to scratch, and start copying the content for today's workshop because it will take a while:
cds cp -r $BI/ngs_course/human_variation . &
Also, start IGV (see etherpad), chose "hg19" as your reference genome. In your spare time, use "File -> Load from URL" to open these URL's:
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12891.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12892.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12878.chrom20.GATK.vcf http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12891.chrom20.GATK.vcf http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12892.chrom20.GATK.vcf http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12878.chrom20.samtools.vcf http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12891.chrom20.samtools.vcf http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12892.chrom20.samtools.vcf
Learning Objectives:
- Understand common genome variants in diploid organisms in the context of a population of individuals
- Understand the tools and techniques to genotype individuals with NGS data from variant calls
- Understand common complexity reduction techniques, how to evaluate their performance, and their impact on variant data
- Understand the tools and techniques to annotate, filter, and perform set analysis on variants
Here is a link to the pdf of the presentation we'll be using in today's class (I'll have printed copies for participants at the class). This wiki page also has the PPT version as an attachment.