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

Oat Landrace Diversity (OLD) Panel phenotypes, genotypes, and metadata from: Rahman et al. (2024) "A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment".
"File S1" and "File S2" include population metadata and phenotypic (environmental) data used in association mapping, of which mapping results are listed in "File S3".
"Rahman_et_al_2024_Metadata.geojson" is geographical information of OLD Panel accessions surveyed in this study.
"SBATCH_RUN_nsgc_deepvariant_glsnexus.sh" and "RUN_nsgc_deepvariant_glsnexus.sh" 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). "DeepVariantWGS.yml" is the config file for running GLNexus.
"nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf" is the final genotype file described in the study.

Oat Landrace Diversity (OLD) Panel表型、基因型及元数据，源自Rahman等（2024年）发表的《全球陆地 oats（Avena sativa L.）品种群体的构建：适应性变异、关联图谱绘制及性状部署的发现资源》。其中，“File S1”与“File S2”包含用于关联图谱绘制的种群元数据及表型（环境）数据，关联图谱绘制结果列于“File S3”。“Rahman_et_al_2024_Metadata.geo”为本研究中调查的OLD Panel品种群体的地理信息。“SBATCH_RUN_nsgc_deepvariant_glsnexus.sh”与“RUN_nsgc_deepvariant_glsnexus.sh”为SciNet集群中基于GBS对齐的变异调用及过滤的脚本。重要提示：请勿在$HOME目录中提取容器，而应将其置于主路径（以便在SciNet集群中使用）。Google DeepVariant生成“deepvariant_1.6.0.sif”（运行命令：singularity pull docker://google/deepvariant:1.6.0）；GLNexus生成“glnexus_v1.4.1.sif”（运行命令：singularity pull docker://google/glnexus:1.4.1）。“DeepVariantWGS.yml”为运行GLNexus的配置文件。“nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf”为研究中描述的最终基因型文件。