Convert phased vcf to Chromosome/scaffold + Tag Haplotype Matrix
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6 weeks ago
QPaps04 ▴ 40

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!

vcf phased haplotypes shapeit bcftools • 233 views
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Seems like there is a function called hapsFromVCF which is in fineradstructure - did you try that?

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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.

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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!

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Ok thank you for your help :)

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