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evotools / hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
GNU General Public License v3.0
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EHH not calculated #42

Open shreyashruti opened 6 years ago

shreyashruti commented 6 years ago

Hi I am not able to calculate EHH for a few loci. The EHH output files get generated but the file shows:

EHH not calculated (<MAF)
iHS: -nan
MAF: 0

How to rectify this error? @prenderj @camaclean

camaclean commented 6 years ago

Hi,

Use --minmaf 0.

-Colin

camaclean commented 6 years ago

I've set the default to 0 for EHH in Pull #43, rather than 0.05 as in ihs scans.

shreyashruti commented 6 years ago

Hi I tried. But the same error. EHH is still not calculated even after changing the minmaf to 0.0 What could possibly be wrong? @camaclean

camaclean commented 4 years ago

If the MAF is 0, then either ehh_0 or ehh_1 is undefined. There is no EHH decay for a nonexistent core. A nan is expected in this case as a core with a MAF of 0 is not a valid input.