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7.6 years ago
I am trying to take the screenshots of the regions of my interest loading aligned BAM file into IGV through command line. I've found very useful threads on this forum (Automated Plotting Of Seq. Reads In A Bam File). But I am interested to get a screenshot which shows bases in reads. The answers provided in the link is useful for getting screenshot 'showing mismatched bases'. I've gone through IGV webpage and found this and I've included
show all bases command in
batch_file.txt but no use. Isn't it possible to get the screenshot which shows bases in reads through command line?
Not that I know of.
I tried several ways and at last I gave up on this. But is it possible to take screenshot covering the entire depth of a position through command line with little bit high clarity?
I also could not get IGV to display bases, but you could have a look at the much more basic
samtools tview. You can at least get ASCII or HTML...
Thank you. But the output is somewhat obscure for me. I've looked at the region
chr12:46231462and the html file is showing
If I understand it correct, the first column is
chr12:46231462, is it?
Yes, I think
-pspecifies the first column.