I would like to create a figure plotting SNP density for each chromosome from a vcf file. All I have on hand now is the vcf file after the SNP call. If anyone knows of any software suitable for this, please tell me.
Otherwise, any help or advice would be much appreciated. It must be doable because I see plenty of published papers with SNP density plotted against chromosome position, but I can't figure out how to do it myself.
Thank you very mach.