Is There A Way To See An Alignment In A Text File?

Question

[diltsjeri]

I know I can view a BAM in IGV, but I'm interested in working with a text file. Is there a way to see an alignment in a text file?

Thanks!

Answer 1

[Pierre Lindenbaum]

use samtools tview http://samtools.sourceforge.net/samtools.shtml

I also wrote a standalone/streaming version http://plindenbaum.blogspot.com/2011/07/text-alignment-viewer-using-samtools.html

[diltsjeri]

Thanks. I will give it a try.

[Matt Shirley]

I second this. For viewing alignments quickly and simply, samtools tview provides everything you need.