Create 10,000bp windows for a SNP file and assign each SNP to its respective window
I have a tab file with 700k SNPs (results from BayPass analysis of p-values for Genotype x environment association). I want to create 10k bp window intervals for each of the chromosome/contig and assign each SNP to its corresponding window.
This is the file I have (sample):
Chromosome SNP bf.db Chr_1 2007 -22.5 Chr_1 7200 16.05 Chr_1 11500 12.05 Chr_1 18000 61.05
This is what I need:
Chromosome SNP bf.db. window Chr_1 2007 -22.5 0-10000 Chr_1 7200 16.05 0-10000 Chr_1 11500 12.05 10001-20000 Chr_1 18000 61.05 10001-20000
I can create windows using bedtools makewindows, but I do not know how to assign each SNP to it’s corresponding window.
• 38 views
Read more here: Source link