This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tool: Pybamview

This tools is work in progress but looks already to be very useful for viewing short tandem repeats (STRs)/insertion-deletions (INDELs) found in high throughput sequencing. It combines the best properties of samtools tview and graphical browsers, such as UCSC genome browser and IGV. Access can be found via the main web page for the project, but I suggest reading the accompanying blog post that goes into the conception of the idea for the project and gives details on the Python code used to run it. Really excellent! Give it a go and provide feedback.

Main website: http://melissagymrek.com/pybamview/

Descriptive and interesting blog post: http://melissagymrek.com/python/2014/01/30/pybamview.html

I came across this via a retweeted tweet from Melissa Gymrek (@mgymrek).

python bam
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updated by Ram Ram • written by Ian Ian

Although I had some problems to actually run it due to having hardcoded paths embedded into the code.

This code only works if you install with sudo and that happens to place the program into /usr/local

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written by Istvan Albert Istvan Albert

Really nice blog post and neat example of a useful hack. I've always been fond of tview and wish more tools would just do a few things really well.

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written by Matt Shirley Matt Shirley

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