Tuesday, 8 May 2012

I love IGV!

Well sorry for the proclamation

But I think it's really nice that you have a relatively small footprint for a application that's cross platform.

anyway I needed to view a few regions of a merged bam file that's aligned to hg18 from 1000 genomes project.
You would think I might have copies of the hg18 lying around on every server so that I can just use 'samtools tview in.bam ref.fasta'

But unfortunately I don't and I am not really looking forward to downloading the hg18 just for a verification exercise.

Luckily I remembered that IGV has prebuilt human genome references that's available on the fly.
with a few clicks, I was happily viewing the regions of interest. (I downloaded the compiled binary instead of using the 'launch from browser' option but that would have been cool too)

among the list of reference human genomes avail there was actually one available for 1KG specifically. How cool is that?

Go on take the application for a run if you haven't!


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Datanami, Woe be me