Question: How to calculate SNP density for sliding windows across a VCF file in galaxy?
gravatar for Guy Reeves
3.0 years ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:


I am trying to think of a way of calculate the number of SNPs per 5kb sliding windows across the reference genome from a VCF file. 

Can any body suggest a workflow or a  to tool to do this efficiently within galaxy ? 


It seams like it should be possible but I cannot think of a way. 


Ideally,  it would be possible to specify not only the window size but also the degree of window-overlap (it is fine to ignore deletions with respects to ref).Thanks Guy

sliding-window galaxy vcf • 1.8k views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by Guy Reeves1.0k
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Guy,

Try the tool "Make windows" to create a reference bed file for input to VCF tools that tabulate counts. If you come up with a good workflow, please consider publishing it on Main.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
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