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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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norm --xpnsl --bp-win output head or explanation #78

Open anhong11 opened 2 years ago

anhong11 commented 2 years ago

Hey,

I run norm --xpnsl with --bp-win, can you help me explain the meaning of each column? BTW, if I have pop_ref vs. pop1 and pop_ref vs. pop2 to find the selective sweep in pop1 and pop2, and then try to compare the selective sweep in pop1 and pop2, should I normalize them together or normalize pop1 and pop2 separately?

Thanks!

szpiech commented 2 years ago

Hi there,

The columns are

<win start> <win end> <# scores in win> <frac scores gt threshold> <frac scores lt threshold> <approx percentile for gt threshold wins> <approx percentile for lt threshold wins> <max score> <min score>

Hope this helps!

anhong11 commented 2 years ago

Hey, Thanks for your quick response!

Does the "frac scores gt threshold" mean "the fraction of XP-nSL scores >2" described in your Evolution Letters paper? Basically, I try to get the information showed in the Table 3 of your paper

szpiech commented 2 years ago

Yes, that's correct.