Question: About command line IGV screenshot
0
gravatar for venu
4.1 years ago by
venu6.3k
Germany
venu6.3k wrote:

Dear all,

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 C: 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?

Thank you.

igv screenshot • 2.0k views
ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 4.1 years ago by venu6.3k

Not that I know of.

ADD REPLYlink written 4.1 years ago by Madelaine Gogol5.1k

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?

ADD REPLYlink modified 19 days ago by RamRS25k • written 4.1 years ago by venu6.3k
2

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...

samtools tview -d H -p c1:10000 my.bam > my-region-of-interest.html
ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by thackl2.7k

Thank you. But the output is somewhat obscure for me. I've looked at the region chr12:46231462 and the html file is showing

46231471     46231481      46231491     46231501     46231511

If I understand it correct, the first column is chr12:46231462, is it?

ADD REPLYlink modified 19 days ago by RamRS25k • written 4.1 years ago by venu6.3k

Yes, I think -p specifies the first column.

ADD REPLYlink modified 19 days ago by RamRS25k • written 4.1 years ago by thackl2.7k
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