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evotools / hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
GNU General Public License v3.0
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VCF support - or conversion script? #15

Closed zeeev closed 8 years ago

zeeev commented 8 years ago

Hi Neil,

I have some large beagle-phased VCF files I would like to run through HapBin. Do you have VCF support?

prenderj commented 8 years ago

Hi Zev

It is a bit buried in the README but you can convert from VCF to impute format using VCFtools with the --impute flag.

http://vcftools.sourceforge.net/man_latest.html#OUTPUT%20OPTIONS

Cheers James

zeeev commented 8 years ago

thanks.