Variable sites VCF files

These files contain sites with a high posterior probability (> 0.8) of being polymorphic in the 8-sample dataset (4 samples from each species), along with their genotype likelihoods in these samples as estimated by ANGSD (http://popgen.dk/wiki/index.php/ANGSD). Genotype likelihoods were estimated using the GATK model (-GL 2). The probability of a site being variable was estimated using ngsStat (https://github.com/mfumagalli/ngsTools), based on posterior probabilities calculated using the genotype likelihoods and the site frequency spectrum estimated from high quality sites (minimum mapping quality 1, minimum quality 20, minimum 3 samples with data, minimum depth 9) within each species.

本批数据集文件包含8样本数据集（每个物种含4个样本）中具有高后验概率（>0.8）的多态性位点，以及由ANGSD（http://popgen.dk/wiki/index.php/ANGSD）估算得到的这些样本中的基因型似然值。基因型似然值通过GATK（Genome Analysis Toolkit）模型（参数设置为-GL 2）估算得到。位点的变异概率由ngsStat工具（https://github.com/mfumagalli/ngsTools）估算得出，其计算依据为：通过基因型似然值计算得到的后验概率，以及从各物种内的高质量位点（最小比对质量值1、最小碱基质量值20、至少3个有测序数据的样本、最小测序深度9）中估算得到的位点频率谱（Site Frequency Spectrum，SFS）。