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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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Column Header info #53

Closed CSGallagher closed 3 years ago

CSGallagher commented 3 years ago

Hello, I just need information about the column header produced by norm --ihs. From parts of the manual and different questions, I can tell that it's

WINSTART WINSTOP. N.SNPS.WINDOW probably.fraction.gt.threshold. PERCENTILE ????

What is the last column that ranges in values from 1-4? Is the fourth column interpreted correctly as being the fraction greater than critical threshold? Apologies ahead of time if this is written elsewhere.

COMMAND RUN: norm --ihs --bp-win --files ./chr1.ihs.out ./chr2.ihs.out ./chr3.ihs.out ./chr4.ihs.out ./chr5.ihs.out ./chr6.ihs.out ./chr7.ihs.out ./chr 8.ihs.out ./chr9.ihs.out ./chr10.ihs.out ./chr11.ihs.out ./chr12.ihs.out ./chr13.ihs.out ./chr14.ihs.out ./chr15.ihs.out ./chr16.ihs.out . /chr17.ihs.out ./chr18.ihs.out ./chr19.ihs.out ./chr20.ihs.out ./chr21.ihs.out ./chr22.ihs.out

OUTPUT [ rsltSelscan]$ head chr2.ihs.out.100bins.norm.100kb.windows 1 100001 15 0 100 1 100001 200001 302 0.013245 100 2 200001 300001 180 0.00555556 100 2

szpiech commented 3 years ago

Hi there,

Sorry this is confusing, compounded by some typos in the README. The fourth column is the frac greater than the critical threshold and the last column is the max |iHS| in the window. Although I just noticed that this was coded as an int for some reason, so until I change that it is giving the floor[max |iHS|].

CSGallagher commented 3 years ago

Thank you so much for the speedy response and clarification!