Whole-genome sequencing of the Sorghum Asssociation Panel
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circos - Circos configuration and execution scripts
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Fst - scripts for Fst calculations
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genomic_prediction - genomic selection scripts
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gwas - scripts for GEMMA
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hecaton - scripts for copy number variant calling
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impute_filter - Beagle and BCFtools scripts
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metrics - LD, nucleotide diversity, PCA
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misc_scripts - snpEff, extract gene features from SNPs
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variant_calling - scripts for GATK variant calling pipeline
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Gene features were extracted using https://github.com/jlboat/features_from_snps
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QTL were isolated from the Sorghum QTL Atlas using https://github.com/jlboat/query_qtl_atlas