The bash codes here include major steps of the analysis procedure for genotyping and identifying targeted SNPs using Genome Analysis Toolkit (GATK) Haplotype Caller for the 48 samples in this study. Suggest to run with nohup.
Assemblies and variant information described in this manuscript have been deposited at Figshare at the following URL: https://dx.doi.org/10.6084/m9.figshare.26801122 (and will be released upon acceptance of the manuscript for publication). SAM files of raw read data for each of the accessions will be deposited in the NCBI SRA database under bioproject PRJNA605472.
(This will be updated later.)