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?