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.
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.
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.
Yesterday we went through how to launch IGV on your local computer (IGV tutorial).
| Cheatsheet of what to do. |
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.