I would like to quickly have a look to a few hundred images of reads mapped to a reference, for a list of a few hundred regions.
What I've got so far is a file with a list of regions "chrname:start-end", and I am simply using samtools tview for them like this:
cat peaks.txt | while read i; do echo -e "g$i\n." | samtools tview my.bam my.ref.fa.gz; done
The "." at the end is to switch of the dots in the tview configuration. I use Ctrl+C to go to the next region.
Is there a better way to do this? Maybe something that generates image files?