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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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Allele frequency versus core haplotype frequency #57

Open paolo002 opened 5 years ago

paolo002 commented 5 years ago

Hi, are the values in the column labelled as "Freq" in the output representing allele frequency or core haplotype frequency? Can the values be different between iHS and XPEHH output?

Thanks Paolo

prenderj commented 5 years ago

Sorry dont quite follow. iHS is calculated around a single variant so that the allele is the core haplotype

On Tue, 23 Apr 2019 at 10:23, paolo002 notifications@github.com wrote:

Hi, are the values in the column labelled as "Freq" in the output representing allele frequency or core haplotype frequency? Can the values be different between iHS and XPEHH output?

Thanks Paolo

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