Question: Visualizing & plotting variant reads within BAM files programmatically?
gravatar for steve
2.7 years ago by
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
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

I've written a BAM2SVG:

enter image description here

and a BAM2raster:

enter image description here

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum120k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1120 users visited in the last hour