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