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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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no standardized IHS output? #48

Closed jkreinz closed 4 years ago

jkreinz commented 4 years ago

Hi again Zack,

Sorry to bug you again but I've gone through the manual and the paper and am still looking for clarification.

The manual says <locusID > <physicalPos > <’1’ freq > <ihh1 > <ihh0 > < unstandardized iHS > is the format of the iHS output. From the paper and manual, I would have expected a standardized iHS column as well. Is this not explicity output by selscan?

Thanks! Julia

szpiech commented 4 years ago

For normalization, you will want to use the norm program. Since all contigs/chrs should be normalized together, you should pass all of them to norm at the same time. e.g. norm --ihs --files chr1.ihs.out chr2.ihs.out ... chrN.ihs.out