Question: Keeping loci those have specific number of SNPS
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gravatar for safiq713
12 days ago by
safiq7130
safiq7130 wrote:

Dear all

I want to keep some loci, only those loci has 4 SNPS (specific number of SNPS). I want to make skyline plot from ddRAD data. Do you have any idea how can go forward

Thanks a lot for your help

skylineplot • 66 views
ADD COMMENTlink modified 12 days ago • written 12 days ago by safiq7130

may be you can create sliding windows and count SNPs within them and keep the ones that has more than 'n' SNPs. and then merge overlapping windows post-hoc to have a consensus loci. This can be achieved by bedtools and a bit of scripting. I am not aware of any tools that does this.

ADD REPLYlink written 12 days ago by geek_y11k
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