How to analyze tree sequence data? #541
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I'm not sure how to proceed after getting results from tsinfer. I created a tsinfer SampleData object using 4 human individuals. 1 population. 59152 variants. The results: Results from tsinfer on the sample data: Is there guidance on how to make sense of the resultant tree sequence data? |
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There's a brief section in https://tsinfer.readthedocs.io/en/latest/tutorial.html#analysis Note that the branch lengths in an inferred tree sequence may not be meaningful, so normal tskit statistics will only work properly in "sites" mode (not "branch" mode - see https://tskit.dev/tskit/docs/stable/stats.html#mode and https://www.genetics.org/content/215/3/779). If you want to use branch lengths in the trees, you should run |
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There's a brief section in https://tsinfer.readthedocs.io/en/latest/tutorial.html#analysis
Note that the branch lengths in an inferred tree sequence may not be meaningful, so normal tskit statistics will only work properly in "sites" mode (not "branch" mode - see https://tskit.dev/tskit/docs/stable/stats.html#mode and https://www.genetics.org/content/215/3/779).
If you want to use branch lengths in the trees, you should run
tsdateon the resulting tree sequence: https://tsdate.readthedocs.io/en/latest/