Variant Calling Files supporting leptospira analysis

This data set contains the results of a variant calling analysis performed on 20 samples named X_SX for sample 1 to 16 and named B3288_2 B3288_8 B3288_10 and B3288_16 for samples named 17 to 20.

All variant calling analysis were performed with Sequana variant calling pipeline (https://github.com/sequana/variant_calling) but only the final VCF files are provided in this dataset. One VCF file per sample and per reference genome used. There were 273 core genomes used; Therefore we have here 273 time 20 VCF files. In the summary directory one can also find the CSV files for SNPs and INDELs that were extracted from the VCF files using several filtering (depth of 10, strand balance >0.2, min frequency >=0.5).

More information and notebooks generating and using those files can be found here: https://github.com/biomics-pasteur-fr/manuscript_capture_leptospira/   A tagged version of this github repository is provided as version 1 : manuscript_capture_leptospira-1.tar.gz

本数据集包含20个样本的变异调用分析结果，其中样本1至16命名为X_SX，样本17至20分别为B3288_2、B3288_8、B3288_10及B3288_16。

所有变异调用分析均采用Sequana变异调用流程（https://github.com/sequana/variant_calling）完成，本数据集仅提供最终的变异调用格式（VCF）文件。每个样本对应每一种使用的参考基因组均生成一个独立的VCF文件，本次分析共使用273个核心基因组，因此本数据集总计包含273×20个VCF文件。在summary目录下，还可获取通过多重过滤（测序深度≥10、链平衡值>0.2、最小等位基因频率≥0.5）从VCF文件中提取得到的单核苷酸多态性（SNP，Single Nucleotide Polymorphism）与插入缺失变异（INDEL，Insertions and Deletions）对应的逗号分隔值（CSV）文件。

更多相关信息以及生成、使用这些文件的Jupyter分析笔记本（notebooks）可在此处获取：https://github.com/biomics-pasteur-fr/manuscript_capture_leptospira/ 该GitHub仓库的带标签版本以版本1的形式提供：manuscript_capture_leptospira-1.tar.gz