Question: Visualizing & plotting variant reads within BAM files programmatically?
0
gravatar for steve
2.7 years ago by
steve2.0k
United States
steve2.0k wrote:

I am looking for essentially the functionality mentioned here; I want to automatically create snapshots of images of reads within a BAM file at specified loci. I know that IGV can do this, but in my experience the results from scripting IGV for this are lackluster since there can be a lot of variability as far as the number of reads on screen and resolution needed for each variant. I also saw that samtools tview has the same functionality. The answers in that previous question are a bit old now, I was hoping that something new might be available? Maybe a Bioconductor package? My searches so far have not found anything quite like this. My immediate needs are for snapshots / static plots of the reads, but ultimately I think this would be a nice application for something like Plotly to enable interactive browsing as well.

alignment • 1.2k views
ADD COMMENTlink modified 2.7 years ago by Pierre Lindenbaum120k • written 2.7 years ago by steve2.0k
4
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

I've written a BAM2SVG: https://github.com/lindenb/jvarkit/wiki/Bam2SVG

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and a BAM2raster: https://github.com/lindenb/jvarkit/wiki/Bam2Raster

enter image description here

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum120k
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