Inferring whole-genome histories in large population datasets: inferred tree sequences for Simons Genome Diversity Project

<p>Tree sequences inferred for the SGDP autosomes using&nbsp;<a href="https://tsinfer.readthedocs.io/">tsinfer</a>&nbsp;version 0.1.4 and compressed using&nbsp;<a href="https://tszip.readthedocs.io/en/stable/">tszip</a>. Tree sequences can&nbsp; be decompressed as follows:</p> <pre><code class="language-bash">$ tsunzip sgdp_chr1.trees.tsz</code></pre> <p>Once decompressed, trees files can be loaded and processed using&nbsp;<a href="https://tskit.readthedocs.io">tskit</a>.&nbsp;</p> <pre><code class="language-python">import tskit ts = tskit.load("sgdp_chr1.trees") # ts is an instance of tskit.TreeSequence print("Chromosome 1 contains {} trees".format(ts.num_trees))</code></pre> <p>Metadata associated with individuals and populations was derived from the original&nbsp;<a href="https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/SGDP_metadata.279public.21signedLetter.samples.txt">source</a>&nbsp;and converted to JSON form. For example, to access individual metadata we can use:</p> <pre><code class="language-python">import tskit import json ts = tskit.load("sgdp_chr1.trees") ind = ts.individual(0) metadata_dict = json.loads(ind.metadata)</code></pre> <p>The metadata_dict variable will now contain&nbsp;all the metadata for the individual with ID 0 as a dictionary. Metadata associated with populations can be found in a similar way. Population IDs are associated with individuals via their constituent nodes. For example,</p> <pre><code class="language-python">pop_metadata = [json.loads(pop.metadata) for pop in ts.populations()] ind_node = ts.node(ind.nodes[0]) ind_pop_metadata = pop_metadata[ind_node.population]</code></pre> <p>After this, the&nbsp;ind_pop_metadata variable will contain the population level metadata for individual ID 0.</p> <p>The full data pipeline used to generate these tree sequences and associated metadata is available on <a href="https://github.com/mcveanlab/treeseq-inference/tree/master/human-data">GitHub</a>.</p>