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.