Supplementary Data - Haplotype-based inference of recent effective population size in modern and ancient DNA samples

<p>This repository contains the simulated data analyzed in our manuscript titled "Haplotype-based Inference of Recent Effective Population Size in Modern and Ancient DNA Samples".The data is split into 7 datasets.&nbsp;</p><p><strong>- demographies.tar.gz</strong>: the simulated demographic models.<br><strong>- modern_data.tar.gz:</strong> simulated SNP-araray data. The genotypes were simulated under 4 demographic histories (see demographies.tar.gz) for 256 samples and under 10 different random seeds (Replicate 1-10). Additionally, Replicates 11 and 12 include simulations at larger sample sizes. Note that the results at lower sample sizes can be obtained by keeping the first N samples of the simulated files.<br><strong>- true_ibd.tar.gz :</strong> This dataset contains the IBD segments from the simulated modern_data (ground truth from ARGON simulator).<br><strong>- ancient_data.tar.gz</strong> dataset contains simulated aDNA data. The dataset contains data simulated at different coverages (MISSING_$M, where $M = exp(-coverage)), sample sizes, demographic models, and random seeds. Split into three parts. See below for instructions on how to reconstruct the dataset.&nbsp;<br><strong>- structure.tar.gz</strong> and<strong> admixture.tar.gz :</strong> contain the data simulated under more complex demographic histories involving 2 isolated populations (structure) or a single population undergoing a recent admixture event (admixtuer.tar.gz). The manuscript provides more details about the demographic histories.<br>- <strong>imputed.tar.gz</strong> dataset contains simulated imputed aDNA data. Each region was simulated independently. Each folder corresponds to a chromosome arm and contains:<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.anc_array.npy: list of the SNPs included in the analysis (simulating a 1240k array)<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.glimpse.vcf.gz: phased ancient population data as phased by GLIMPSE v1<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.glimpse.vcf.gz.csi: index for the above VCF file<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.imputed.vcf.gz: imputed ancient population data (unphased, including dosages and genotype posteriors)<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.imputed.vcf.gz.csi: index file for the above VCF<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.map.gz: genetic map for GLIMPSE (tab-separated format: pos chr cM)<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.ref.tsv.gz: file used for calculating genotype likelihoods with BCFtools mpileup command to use as input for GLIMPSE (format: chromosome position ref_allele,alt_allele)<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.ref.tsv.gz.tbi: index for the above file<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.ref.vcf.gz: simulated sequencing data from the reference panel<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.ref.vcf.gz.csi: index file for the above VCF<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.target_ground_truth.vcf.gz: simulated sequencing data for the ancient population (ground truth)<br>&nbsp;&nbsp;&nbsp;&nbsp;- datalist.txt: list of genotype likelihood files for each target individual (to be used for merging into a single file)<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.temp.map.gz: genetic map for data creation with msprime simulator (format: chr&nbsp; position&nbsp; rate(cM/Mb) cM)<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.tree -&gt; msprime simulator output containing all samples, both reference panel samples and ancient population samples<br>&nbsp;&nbsp;&nbsp;&nbsp;- data.vcf.gz: VCF containing ground truth sequencing data, phased genotypes for reference panel samples and for ancient population samples<br>&nbsp;&nbsp;&nbsp;&nbsp;- dataref.fa.fai: index for reference fasta file used during reads creation</p><p>&nbsp;</p><p>Note that some of the datasets have been split into multiple parts, for example admixed.tar.gz &nbsp;has been split into three different parts admixed.tar.gz-part-aa, admixed.tar.gz-part-ab, and admixed.tar.gz-part-ac<br>You can get the data by typing:</p><p>cat admixed.tar.gz.part-* &gt; admixed.tar.gz</p><p><br>&nbsp;</p>