Variant calls associated with "Parallel adaptation of rabbit populations to myxoma virus"
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Alves, J., & Jiggins, F. (2019). Variant calls associated with "Parallel adaptation of rabbit populations to myxoma virus" [Dataset]. https://doi.org/10.17863/CAM.35707
Compressed archive containing three files associated with the manuscript "Parallel adaptation of rabbit populations to myxoma virus". File 1 (rabbit_dataset.vcf) is a VCF file containing genotype calls inferred from the exome-sequencing of 152 European rabbit samples of modern and historical populations from Australia, France and the United Kingdom, collected between 1856 and 2013. Samples were collected to investigate adaptation to myxoma virus in rabbits by comparing pre and post-myxomatosis populations. Each sample name is composed by a code of four strings of abbreviations connected by an underscore (e.g. M_AU_NSW_bh1). The first string states the sample type (M for modern and H for historical), the second refers to the country of origin (AU for Australia, FR for France and UK for the United Kingdom), the third refers to the state (Australia), department (France) or county (United Kingdom), and the fourth string represents the sample location (e.g. city, village) followed by the sample number (to distinguish samples collected in the same location). The VCF was generated using GATK, version 3.5 only for all samples with a minimum coverage of 5x. Details concerning samples, sequencing, bioinformatic pipeline pre-genotype calling and variant/genotype filters are available in the supplementary material of the manuscript and in the header of the VCF file. File 2 (rabbit_dataset.vcf.idx) is the VCF index file. File 3 (rabbit_dataset_allelecount.txt) is an allele count of all SNPs for each historical and modern population inferred from the VCF file. All the variant calls that are described in detail in: Alves et al 2019 Parallel adaptation of rabbit populations to myxoma virus. Science.
The VF file can be used by GATK: https://software.broadinstitute.org/gatk/
Rabbit, VCF, Myxomatosis
This record's DOI: https://doi.org/10.17863/CAM.35707
Attribution 4.0 International, Attribution 4.0 International, Attribution 4.0 International, Attribution 4.0 International