Overview whole genome and complexity reduction methods (GVA14)

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. You're also better off doing this in an idev just in case you want to do some computation...

idev -m 180 -q normal -A CCBB
 
<if your idev shell comes up quickly, do this - otherwise open a new connection to lonestar and start the copy on a head node>
 
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.