Question: Is There A Simple Sam Viewer, That Can View Copy/Pasted Sam Formatted Alignment Info?
gravatar for jnfass
7.2 years ago by
jnfass30 wrote:

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?

viewer bam visualization sam • 1.8k views
ADD COMMENTlink written 7.2 years ago by jnfass30

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.

ADD REPLYlink written 7.2 years ago by jnfass30
gravatar for SES
7.2 years ago by
Vancouver, BC
SES8.2k wrote:

Have you tried Tablet? The only negative thing I can say about Tablet is that it's difficult to google, but it will detect updates automatically and install them so you don't have go searching for it online. Two other solutions you might want to try are BamView and Samscope.

ADD COMMENTlink written 7.2 years ago by SES8.2k
gravatar for madkitty
7.2 years ago by
madkitty580 wrote:

you can just call samtools and add view | more at the end of your code .. I think it should work

ADD COMMENTlink written 7.2 years ago by madkitty580

I think you would want "tview" to view the alignment, "view" is for conversion, if I'm not mistaken.

ADD REPLYlink modified 7.2 years ago • written 7.2 years ago by SES8.2k
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