I've got some very deep (at particular locations) BAM files, which always tends to cripple alignment viewers like IGV, tview, etc. Sometimes I want to see what a particular read's alignments look like, and while it's easy to grep those lines out of a SAM file, it's problematic to find them among the alignments in a viewer. For example, IGV allows you to search by QNAME (read ID), but it'll only find the alignments if they're displayed, which they're often not in very deep locations (because it's necessary to set a reasonable max depth in order to have decent performance).
I can grep the header and appropriate SAM lines out, convert to sorted BAM, index, then load a new track, but that gets tedious. Why shouldn't I be able to paste in a couple lines of SAM and see the alignments in the browser / viewer, immediately? Does anyone know of a viewer that has this capability?
2 answers
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To clarify, I'm familiar with all of the suggested alignment viewers. What I want is to be able to paste some SAM-formatted text into an input field, and immediately see the alignment features encoded by that text.