Whole genome re-sequencing workshop data: filtered vcf file, bed file, edited fam file and bim file for population genomics workshop

Whole genome re-sequencing data analysis workshop datasets. The files are necessary inputs for the workshop in https://github.com/PoODL-CES/Genomics_learning_workshop Tools and scripts listed in the https://github.com/PoODL-CES/Genomics_learning_workshop repository. The files contain filtered variants from the "raw" variants in https://zenodo.org/records/15173226 filters used are: minimum Q 30 minimum GQ 30 no Indels variants flagged as "PASS" Hardy Weinberg chi square p value of 0.05 Individuals with more than 60% missing data removed loci with more than 60% missing data removed mean depth was mid 95 percentile of depths across loci and all zoo born individuals removed from the dataset This a part of the vcf file with data of chromosome E2 from:Khan, A., Patel, K., Shukla, H., Viswanathan, A., van der Valk, T., Borthakur, U., Nigam, P., Zachariah, A., Jhala, Y.V., Kardos, M. and Ramakrishnan, U., 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proceedings of the National Academy of Sciences, 118(49), p.e2023018118. The reference genome is from : Shukla, H., Suryamohan, K., Khan, A., Mohan, K., Perumal, R.C., Mathew, O.K., Menon, R., Dixon, M.D., Muraleedharan, M., Kuriakose, B. and Michael, S., 2023. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. GigaScience, 12, p.giac112.全基因组重测序数据分析工作坊数据集。本数据集为https://github.com/PoODL-CES/Genomics_learning_workshop 对应工作坊的必需输入文件，配套分析工具与脚本详见该代码仓库：https://github.com/PoODL-CES/Genomics_learning_workshop。 本数据集的变异位点源自https://zenodo.org/records/15173226 中的“原始”变异集，经过如下筛选流程： 1. 最低测序质量值（Quality Score, Q）≥30 2. 最低基因型质量值（Genotype Quality, GQ）≥30 3. 剔除插入缺失（Insertions and Deletions, Indels）变异 4. 保留标记为“PASS”的合格变异位点 5. 哈迪-温伯格卡方检验P值≥0.05 6. 移除缺失数据占比超过60%的个体 7. 移除缺失数据占比超过60%的遗传位点 8. 以所有遗传位点测序深度的95%分位数中位数作为平均测序深度阈值 9. 移除所有动物园圈养繁育个体。 本数据集为下述文献中E2号染色体对应的VCF（Variant Call Format）文件子集：Khan, A.、Patel, K.、Shukla, H.、Viswanathan, A.、van der Valk, T.、Borthakur, U.、Nigam, P.、Zachariah, A.、Jhala, Y.V.、Kardos, M.与Ramakrishnan, U.于2021年发表于《美国国家科学院院刊》的研究《Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers》，该文收录于Proceedings of the National Academy of Sciences, 118(49), p.e2023018118。 本研究所用的参考基因组源自下述文献：Shukla, H.、Suryamohan, K.、Khan, A.、Mohan, K.、Perumal, R.C.、Mathew, O.K.、Menon, R.、Dixon, M.D.、Muraleedharan, M.、Kuriakose, B.与Michael, S.于2023年发表于《GigaScience》的研究《Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation》，该文收录于GigaScience, 12, p.giac112。