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haploid mode without ancestor allele #29

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Yiguan opened this issue Jun 26, 2020 · 0 comments
Open

haploid mode without ancestor allele #29

Yiguan opened this issue Jun 26, 2020 · 0 comments

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@Yiguan
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Yiguan commented Jun 26, 2020

I am using haploid mode as following:

python ~/diploSHIC/diploSHIC.py fvecSim haploid hard_1.msOut hard_1.test --totalPhysLen 5500

Since i don't know the ancestral allele, I didn't use --ancFileName option. The problem is the output file which contains 15 summary statistics, including maxFDA. If I understand correctly, there would be 11 summary statistics under SHIC mode.

The classifier which contains 15 summary statistics could not be used on sample data which contain 11 summary statistics derived using fvecVcf with haploid mode.

So I think the problem is how to train a classifier with 11 summary statistics using fvecSim.

Thanks!

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