Southern sea otter genotypes
datasetposted on 22.06.2019, 05:23 by Annabel Beichman
This directory contains the filtered genotypes from southern sea otter (Enhydra lutris nereis) sequencing reads (Project number: PRJNA472597, Acc. SRR8597300) mapped to the domestic ferret reference genome (GCF_000215625.1). The files are in vcf format, and the genome was split into 323 chunks to reduce file sizes. Each of the first 1-224 .vcf files contain a single scaffold, and the remaining 225-323 vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz). The reads were mapped, genotypes were called and filtered as described in the README and SI Methods in Beichman et al. 2019.