Repository containing data and code for the guar (Cyamopsis tetragonoloba (L.) Taub.) genotyping and GWAS project. A brief description of the repository contents:
make_consensus_vcf.py script was used to generate the final variant dataset using raw GATK-HC, NGSEP and TASSEL 5 variant calls, make_snp_stats.py script was used with the same inputs to explore the quality statistics of the variant calls.
callset_refinement_filtering.ipynb notebook was used to run variant quality control and construct the final filtered dataset of common variaants.
genetic_analysis.ipynb notebook was used to perform most of the genetic analyses, including PCA, linkage disequilibrium analysis, and generalized linear model-based association analysis.
prepare_farmcpu.py script was used to format input data for FarmCPU tool (Q-Q plot of the resulting p-values is shown in the paper and below).
admix_file_create.py file was used to preprocess genotypes for ADMIXTURE analysis (part of this was done using Hail in the genetic_analysis.ipynb).
guar_stat.R script was used to run statistical analysis of the final data, conduct genome-wide association analysis using the FarmCPU tool, and plot main figures
parse_vcf_fcpu.py script was used to format the final SNP genotype table available as the genotypes.xlsx file in this repository.