--pi not an option

[stsmall]

Hi, I recently started using your code to estimate f2, since I couldnt seem to get AdmixTools to compile correctly. I have got most of the tests listed in the README to work correctly, although --pi doesnt seem to be recognized as an option. I also cant find it listed in the python file as an option. Any plans to update this?

Also I couldnt find the vc2tped.py mentioned in the README so just used VCFTOOLS --plink-tped option.

Any chance you might implement something where --pop option could accept a "file" with a list of which individuals belong to which populations? Currently, it is a bit cumbersome to list all individuals that belong to a population on the command line (e.g., ind1+ind2+ind3,ind4+ind5+ind6) and for calculating f2 needs to be rearranged since it only looks at pops in 1 and 2 position. What about a pairwise calculation for anything involving only 2 pops?

thank you,

[pontussk]

Hi,

Thanks for your note. Please try the attached version of the program that should have the --pi options. THanks for pointing this out.

I recommend using population labels in the first column of the tfam file, that way you can just use these in --pop.

Best, Pontus

On Thu, Nov 3, 2016 at 3:26 PM, stsmall [email protected] wrote:

Hi, I recently started using your code to estimate f2, since I couldnt seem to get AdmixTools to compile correctly. I have got most of the tests listed in the README to work correctly, although --pi doesnt seem to be recognized as an option. I also cant find it listed in the python file as an option. Any plans to update this?

Also I couldnt find the vc2tped.py mentioned in the README so just used VCFTOOLS --plink-tped option.

Any chance you might implement something where --pop option could accept a "file" with a list of which individuals belong to which populations? Currently, it is a bit cumbersome to list all individuals that belong to a population on the command line (e.g., ind1+ind2+ind3,ind4+ind5+ind6) and for calculating f2 needs to be rearranged since it only looks at pops in 1 and 2 position. What about a pairwise calculation for anything involving only 2 pops?

thank you,

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[stsmall]

Hi Pontus, Sorry for being dense, but I dont see an attached version. Could you send me a link to the version please. I also noticed that --FAB option isnt in the code yet a --TDiv option is. What is TDiv? thanks, scott

[pontussk]

Hi,

Try this link: https://drive.google.com/file/d/0BzxpmkTnJX5AcEFuQlZUZHRDdVE/view?usp=sharing

--FAB should be in that version. Tdiv is an experimental option.

On Wed, Nov 9, 2016 at 1:19 AM, stsmall [email protected] wrote:

Hi Pontus, Sorry for being dense, but I dont see an attached version. Could you send me a link to the version please. I also noticed that --FAB option isnt in the code yet a --TDiv option is. What is TDiv? thanks, scott

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