Convert phased vcf to Chromosome/scaffold + Tag Haplotype Matrix
Hello all,
I am wanting to convert a phased vcf to a Chromosome/scaffold + Tag Haplotype Matrix that has the format of this example file to then use for fineRADStructure.
I produced my phased information using SHAPEITv2, which I then subsequently converted to a vcf format. Here is the first three lines of my vcf (excluding the header) the show you the format that need converting:
SUPER_10 182080 . C G . PASS . GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 1|1 0|1 0|0 0|0 0|0 0|1 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
SUPER_10 182095 . T A . PASS . GT 1|1 0|0 0|1 0|1 1|1 0|1 0|0 1|1 1|1 1|1 0|1 1|1 0|1 1|1 1|1 0|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 0|1 0|1 0|0 1|1 1|1 0|0 0|1 1|1 0|0 1|1 0|1 0|1 1|1 1|1 0|1 1|1 0|1 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 0|1 1|1 0|1 0|0 1|1 0|0 0|0 0|1 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|1 1|1 1|1 1|1 0|0 0|1 1|1 1|1 0|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|0 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|0 1|1 1|1 0|1 1|0 0|0 0|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 0|0 1|1 0|1 0|1 0|1 0|1 1|1 0|1 1|1 1|1 0|1 0|1 0|0 0|1 0|0 1|1 0|1 1|1 0|1 1|1 1|1 0|0 1|1 0|0 0|1 1|1 0|1 0|1 1|1 0|1 0|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|0 1|1 0|1 0|0
SUPER_10 182129 . C T . PASS . GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
Thank you in advance for your help.
If you need anymore information to help address the question, please let me know.
Thank you!
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Seems like there is a function called hapsFromVCF which is in fineradstructure - did you try that?
Hello, Yes I have tried that but it doesnt seem to take chromosome information through - so I wanted to try this other format to see if I get a different result.
OK. In that case, I'd maybe contact the authors directly. I think this is quite a niche issue which people here probably won't be able to help you with. Good luck!
Ok thank you for your help :)