This isn't a tutorial as much as it is the first step to our tutorials for today. Hopefully the fact that we are starting this before we get into a presentation and emphasizing how long its going to take impresses upon you that these files really are much bigger and therefore more difficult/expensive to work with from a time perspective if nothing else.

Start File Copy

The most important thing is getting these downloads starting. If you can quickly (<2-3 minutes) get on an idev node great, otherwise start it on the head node.

Suggested iDEV command and copy command

idev -m 180 -q normal -A "UT-2015-05-18"
cds
cp -r $BI/ngs_course/human_variation BDIB_Human_tutorial &

Remember we can add the -v option to the cp command if we like some extra peace of mind that files are actually copying and that our terminal hasn't locked up.

Set Up IGV

Yesterday we went through how to launch IGV on your local computer (IGV tutorial).

Review the specifics of IGV in yesterday's tutorial, or click here for a brief summary

Cheatsheet of what to do.

In IGV, use "file -> load from URL" to open each of the following URLs

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

We will now proceed with the presentation, and hopefully the copy will finish during that.

Human Variant set up

Start File Copy

Set Up IGV