Any Good Bam And Sam Viewer?
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10.2 years ago
Ken ▴ 150

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

viewer sam bam • 34k views
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10.2 years ago
lh3 32k
  • 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.

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

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10.2 years ago

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

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7.2 years ago
madk00k ▴ 350

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?

 

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8 months ago

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

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