Any Good Bam And Sam Viewer?

Question

[Ken]

Hi all, what SAM/BAM viewer are you using? do you have any suggestion on a good BAM/SAM viewer? Thanks in advanced.

Answer 1

[lh3]

• Best overall, especially for checking SNPs across multiple samples: IGV. The major problem to me is IGV does not display inserted sequences (still true?).

• Most beautiful: Tablet. It supports more formats, but does not provide enough information for eye-checking variant calls. I always find IGV to be more convenient for my tasks.

• For ChIP-seq: SeqMonk. Heard good things about it; never used.

• Occasionally handy: samtools' tview (when over slow network or for quick check). One of the few viewers that display inserted sequences (what else besides gap5?). But most users would prefer IGV instead.

• The only assembly editor: gap5. You need to convert BAM to the gap5 format first.

Others: BamView (limited functionality), MagicViewer (not always working) and Gambit (not so mature as others). There are a few more but I forgot the names.

[Matthieu Miossec]

Is it possible for SAMtools tview to omit showing a mapped read for whatever reason?

Answer 2

[Adrian Cortes]

IGV:

http://www.broadinstitute.org/igv/

Answer 3

[Casey Bergman]

Jeremy Leipzig has written a nice review on NGS viewers which may help answer some of your questions: http://jermdemo.blogspot.com/2010/08/ngs-viewers-reviewed.html

Answer 4

[Jeremy Leipzig]

Awesome list of viewers: https://github.com/cmdcolin/awesome-genome-visualization

Answer 5

[madk00k]

Here is a link to my review of BAM/SAM viewers in context of RNA-seq and fusion genes discovery:

Visualizing RNA-seq alignments with fusions: is there anything better than IGV?

Answer 6

[dariober]

Well, since this question came back to the top here's my answer: for BAM and other genomic formats I use my own tool ASCIIGenome