We sequenced 21 tissue samples using whole‐genome resequencing protocols. Illumina library preparation was undertaken by the University of Idaho Genomics and Bioinformatics Resources Core (GBRC; Moscow, Idaho) using the Illumina Nextera library preparation kit following manufacturer's protocols. Samples were PE150‐sequenced on a single S4 lane of a Novaseq 4000X by the University of Oregon G3CF. Samples averaged 114 M reads/sample before filtering.
For this project, samples were genotyped exclusively at the loci used for GT‐seq sequencing. First, samples were aligned to the same genome used when genotyping the RADseq dataset, downloaded from NCBI (SpeTri2.0, accession #GCF_000236235.1, accessed 7/09/2023). Sequences were aligned using bwa mem (Li & Durbin, 2010 (link)). Alignments were sorted and filtered to remove duplicates and exclude improperly paired reads. Genotypes were called in angsd 0.981 (Korneliussen et al., 2014 (link)) using the following settings: ‐minDepth 126 (avg 6×), ‐minInds 16 (76%), ‐minMaf 0.05, ‐postCutoff 0.95 ‐snp‐pval 1e‐6, ‐minQ 20, ‐minMapQ 10. A sites file with the positions of the GT‐seq loci was passed to angsd along with the list of input bamfiles.
For this project, samples were genotyped exclusively at the loci used for GT‐seq sequencing. First, samples were aligned to the same genome used when genotyping the RADseq dataset, downloaded from NCBI (SpeTri2.0, accession #GCF_000236235.1, accessed 7/09/2023). Sequences were aligned using bwa mem (Li & Durbin, 2010 (link)). Alignments were sorted and filtered to remove duplicates and exclude improperly paired reads. Genotypes were called in angsd 0.981 (Korneliussen et al., 2014 (link)) using the following settings: ‐minDepth 126 (avg 6×), ‐minInds 16 (76%), ‐minMaf 0.05, ‐postCutoff 0.95 ‐snp‐pval 1e‐6, ‐minQ 20, ‐minMapQ 10. A sites file with the positions of the GT‐seq loci was passed to angsd along with the list of input bamfiles.
Free full text: Click here
