I have a large number of loci I would like to examine manually with
samtools tview. Rather than typing or copy-n-pasting dozens of coordinates, I was hoping to automate the generation of pileup "images" (text files).
With some experimenting just now, I was happy to learn that if I specify the display option
-d H or
-d T the output can easily be redirected to a file for later inspection. However, it appears that I cannot control the window captured. Changing the width of the terminal window doesn't change the output, nor does adjusting the
-p flag (i.e.
-p chr1:501-700). No matter what,
tview always reports an 80bp window in text or HTML mode.
Is there any way I can adjust this?