PopDel identifies medium-size deletions jointly in tens of thousands of genomes - Variant call sets

This data set contains the variant calls sets generated by different tools for the benchmarks in the paper PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes. It includes the VCFs/BCFs for the following test cases: Random deletion simulation on up to 1000 chromosome 21 samples 1000 Genomes Project deletions inserted into simulated chromosomes 17 to 22 of up to 500 samples HG001 (NA12878) Trio of HG002 + HG003 + HG004 Polaris Diversity cohort Polaris Kids cohort Further, the long and short read reference call sets for HG001 are provided. For HG002 the reference call set and the high confidence regions by the Genome in a Bottle consortium are provided. For details on how the files have been created, please refer to the paper and the script repository on GitHub.本数据集包含为论文《PopDel可同时在数万个基因组中鉴定中等长度缺失》的基准测试所生成的、由不同工具产出的变异调用集（Variant Call Set）。数据集涵盖以下测试场景对应的VCF（变异调用格式，Variant Call Format）/BCF（二进制变异调用格式，Binary Call Format）文件：针对最多1000个21号染色体样本的随机缺失模拟；将千人基因组计划（1000 Genomes Project）的缺失序列插入至多500个样本的17至22号模拟染色体所构建的测试；HG001（NA12878）与HG002、HG003、HG004组成的三人核心家系；Polaris多样性队列；Polaris儿童队列。此外，本数据集还提供了HG001的长读长与短读长参考变异调用集；针对HG002，则同步提供其参考变异调用集，以及由“瓶中基因组”（Genome in a Bottle）联盟划定的高置信度区域文件。若需了解各文件的具体生成流程，请参阅该论文及GitHub上的脚本仓库。