Allele frequency versus core haplotype frequency

[paolo002]

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]

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

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On Tue, 23 Apr 2019 at 10:23, paolo002 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#57>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB5OYGT7VOXRLNE7CI4OMFDPR3IQ5ANCNFSM4HHWEINQ> .