Data from: A global assembly of landrace oat (<i>Avena sativa</i> L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment

<p>Oat Landrace Diversity (OLD) Panel phenotypes, genotypes, and metadata from: Rahman et al. (2024) "A global assembly of landrace oat (<em>Avena sativa</em> L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment".</p> <p><strong>"File S1"</strong> and <strong>"File S2"</strong> include population metadata and phenotypic (environmental) data used in association mapping, of which mapping results are listed in <strong>"File S3"</strong>.</p> <p><strong>"Rahman_et_al_2024_Metadata.geojson"</strong> is geographical information of OLD Panel accessions surveyed in this study.</p> <p><strong>"SBATCH_RUN_nsgc_deepvariant_glsnexus.sh"</strong> and <strong>"RUN_nsgc_deepvariant_glsnexus.sh"</strong> are scripts for variant calling and filtering in SciNet clusters from GBS alignments. IMPORTANT: Do not pull containers in $HOME directory - put them in the main path (for use in SciNet clusters). Google DeepVariant - generates "deepvariant_1.6.0.sif" (RUN: singularity pull docker://google/deepvariant:1.6.0); GLNexus - generates "glnexus_v1.4.1.sif" (RUN: singularity pull docker://google/glnexus:1.4.1). <strong>"DeepVariantWGS.yml"</strong> is the config file for running GLNexus.</p> <p><strong>"nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf"</strong> is the final genotype file described in the study.</p>