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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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Window size selection #46

Closed devenderarora closed 4 years ago

devenderarora commented 4 years ago

Dear Sir, I am working with SNP data and we ran xp-ehh using selscan and it works smooth less. Currently, I am looking for a window size to rerun the same. Is there any way we can set window size to 5kb or so? I will be grateful for any help in this regards. Regards Devender

szpiech commented 4 years ago

Hi there,

The only place that a window size pops up is when using norm to compute the percentage of extreme scores in a region. You can compute this with norm by passing the --bp-win flag, and you can change the size of the window to 5kb with --winsize 5000. Hope this helps.

devenderarora commented 4 years ago

Dear Sir, I tried using --bp-win option as suggested. I am able to get output with </start/> </end/> </no of snp/> </score/> <some window size 5/100> Although this works fine but now I am not able to get any P-value as suggested earlier with norm function in 5kb window file. Any suggestion on this part.

szpiech commented 4 years ago

I'm not sure I know what you are looking for, as xpehh is computed on a site by site basis. The only window option is when looking for clusters of extreme scores with norm --bp-win.