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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?

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2 Answers 2

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Partially a shameless plug. See if ASCIIGenome can help you with that.

To review a number of regions that you saved in, say, a bed file, you can either process them in batch or load BAM(s) and bed file and jump from one bed interval to the next using the next -start command.

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I cross-posted this question on the official samtools issue tracker, and finally got a response.

Looking at the code for the HTML view, I see this and this. So maybe try

COLUMNS=200 samtools tview -d H -p CHR:X-Y aln.bam ref.fasta

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