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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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understand the out file of selscan #35

Closed Lee211 closed 5 years ago

Lee211 commented 5 years ago

The out file of ihs includes the several columns: ID, pos, '1' freq, ihh1, ihh0, unstandardized iHS. i want to know which allele was selected when iHS (the last column) is positive/negative? I do not encode the input file using 0 for ancestral allele and 1 for derived allele. I guess positive iHS represents the allele encoded by '1' was selected, it is may be ancestral (encode by '1') or derived allele (encode by '1'). Is my understand true ???

szpiech commented 5 years ago

I recommend reading through the manual section 4 and Szpiech and Hernandez (2014), where this information is explained. These are available in the github repository. In general when using selscan, more positive values suggest longer and higher frequency haplotypes surrounding the '1' allele, more negative values suggest the same for haplotypes surrounding the '0' allele.