Question: Opening VCFTools Linkage output in HaploView
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gravatar for rc16955
2.1 years ago by
rc1695560
rc1695560 wrote:

Hello all,

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:

enter image description here

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.

ADD COMMENTlink written 2.1 years ago by rc1695560
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