How do I create "data/1kg_gnn.csv"?

[T-Funayama]

I created "1kg_chr20.snipped.trees.gnn.csv" using "human-data/Makefile".
However, "1kg_chr20.snipped.trees.gnn.csv" and "data/1kg_gnn.csv" values did not match.
Would you tell me how to create "data/1kg_gnn.csv", please?

[hyanwong]

Sorry, what do you mean by "did not match"? These are not meant to give exactly the same values. Could you possibly post e.g. the first few lines of each file here, and I can see if they are as you might expect.

Note that you might also be interested in the more recent 1kg+HDGP+SGDP analysis done in https://github.com/awohns/unified_genealogy_paper

[T-Funayama]

Thank you for your response. This is the file which I created.
1kg_chr20.snipped.trees.gnn.csv

Thank you for looking into this.

[T-Funayama]

Hi, could you let me know if you have any updates on this matter ?
I thought I could obtain exactly the same values, because the tool does not seem to use sampling methods such as MCMC algorithm.
Thank you very much for your consideration.

[hyanwong]

Hi - sorry that I didn't spot your follow up here.

You said:

"1kg_chr20.snipped.trees.gnn.csv" and "data/1kg_gnn.csv" values did not match.

Do you mean they did not match each other, or that they did not match our published data.

Note that if you are using the latest version of tsinfer, it has seen improvements to that used in the original paper, so the results will probably be slightly different anyway.