Closed jkreinz closed 4 years ago
Hello, Sorry I haven't updated this information. Indeed the first two columns are physical and genetic distance, respectively. The next two are the ehh for the haplotypes containing the '1' allele and '0' allele, respectively, and the final column should give the ehh for all the haplotypes together.
Great - thanks for the info!
One more question, is it possible to get the length of the haplotype used to calculate iHS? Can I calculate this manually by just looking for where EHH becomes <= 0.05?
Unfortunately, I don't see a super simple way to do this given the ihs output of selscan
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Hi there,
Thanks so much for this software - I've find it extremely useful in my research.
I have a clarifying question about the EHH output. I'm currently using selscan v1.2.0a but have made sure the documentation is consistent with regard to the EHH output with the newest verison. While the documentation describes 4 columns of output for EHH, my output file has 5. For e.g:
I would have considered the first physical distance and the second genetic distance. But then there are three remaining columns, only two of which refer to EHH for allele 1 and allele 0.
Can you please reiterate what these columns represent? Thanks, Julia