A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity

Scripts from paper: https://doi.org/10.1111/tpj.16123

Variant calling:

• code/HCCscrpts/1_Alignment/ - codes for alignment with SpeedSeeq
• code/HCCscrpts/2_HaplotypeCaller/ - codes to run HaplotypeCaller (GATK v. v.4.2.0.0)
• code/HCCscrpts/3_GenomicsDB/ - codes for to create GenomicsDB datastores (GATK v. v.4.2.6.1)
• code/HCCscrpts/4_JointCalling/ - codes joint variant calling and producing VCF files (GATK v. v.4.2.6.1)
• code/HCCscrpts/5_Filter_VCFs/ - codes for variant filtering with Hard-Filtering criteria
• code/HCCscrpts/6_Merge_and_sort_VCFs/ - codes merging and sorting VCFs
• code/HCCscrpts/7_Merge_and_sort_VCFs/ - codes subsetting high confidence variant set
• code/HCCscrpts/8_Merge_and_sort_VCFs/ - codes for imputing confidence variant set

Population analysis:

• code/HCCscrpts/9_Population_analysis/ - codes for population analysis (MAF, LD, nucleotide diversity, variants number per region, PCA)
• code/HCCscrpts/10_GWAS/ - codes for GWSA for days to silking

Data availability:

The additional resequencing data generated as part of this project has been deposited in the European Nucleotide Archive (ENA) under the study accession numbers: PRJEB56265, PRJEB56295, and PRJEB56320. Raw VCF files for all 366 million variants identified in this study, imputed VCF files for the 46 million quality and minor allele frequency filtered variations identified as part of this study and GATK GenomicsDBs files to enable new SNP calling with additional populations have been deposited are available for download from www.maizegdb.org