I wonder if anyone can kindly help.
I've built a reference genome for my species (not annotated or split into chromosomes) so in form of scaffolds and left over contigs. I've then indexed and aligned my RAD data to it which seems to have worked well After building loci, I've exported from STACKS after ref_map build to plink to look at LD, basically I want to remove linked SNP's from further analysis. For 1756 SNP's (first snpand last snp shown below and already filtered on basis of MAF etc), The map file has the 4 columns of info but the last column for bp position runs only from 0 to 9718422 when the genome is 1.2Gbp long
0 32977_106 0 26 0 37087_86 0 9718422
I'm now lost as how I can generate LD data from this when the information in the map file seems peculiar?
Sorry if all sounds naive but can anyone offer a word of advice at ll?