about h4

[vicbp1]

Dear Pontus,

I was trying to understant the parameters for the h4 test (LD option) and I have some doubts

the --LD option is the classic D of LD but what about the LD window? which are the unit for this option? I thought that were cM but the default is 5000 (in the code).

Thank you for your time

[pontussk]

Hi,

--LD defines that midpoint distance for which D is computed and --LDwindow defines a range around that midpoint. You can change the unit using the --morgan option. In our 2015 paper that used the h4 test I ran for example:

python popstats.py --file prefix --pops Yoruba,Onge,Mixe,Surui --morgan --LD 0.000005 --LDwindow 0.000005 --withinfreq

This command would then apply the h4 statistic to pairs of snps within a range of (0.000005-0.000005) to (0.000005+0.000005), i.e. 0 to 0.000010.

Hope that helps. I have not used the h4 statstic much since the 2015 paper. It is potentially powerful but mainly when you have well-ascertained and well-phased data.

/Pontus

On Mon, Aug 20, 2018 at 11:16 AM, vicbp1 [email protected] wrote:

Dear Pontus,

I was trying to understant the parameters for the h4 test (LD option) and I have some doubts

the --LD option is the classic D of LD but what about the LD window? which are the unit for this option? I thought that were cM but the default is 5000 (in the code).

Thank you for your time

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