I have some linkage data obtained with VCFTools, based on a VCF file that was in turn generated from a bunch of bam files each corresponding to the complete genome sequence of an individual of my study species. The command used to generate the linkage data was this:
vcftools --vcf S_ratti_phased.vcf --hap-r2 --ld-window-bp 10000 --out ld_window_10000
The output file generated looks like this:
I would like to be able to visualise these results in some sort of intuitive way, such as with HaploView or a similar program, but I can't figure out how to format this data in such a way that HaploView accepts it. Would anyone have any suggestions? I'm open to any and all advice/suggestions as this is the first time I've tried to do something like this and aren't really sure that I'm on the wrong track.
Thanks in advance
p.s. I have tried to find previous threads about this to no avail, but if I've missed them, apologies and please do point me in the right direction.