Keeping loci those have specific number of SNPS
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
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safiq713 •
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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.