Question: How to calculate SNP density for sliding windows across a VCF file in galaxy?
3.0 years ago by
Guy Reeves • 1.0k
Guy Reeves • 1.0k 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
ADD COMMENT • link •modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by Guy Reeves • 1.0k