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Whole-genome sequencing of the Sorghum Asssociation Panel

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Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
Fst		Fst
circos		circos
genomic_prediction		genomic_prediction
gwas		gwas
hecaton		hecaton
metrics		metrics
misc_scripts		misc_scripts
variant_calling		variant_calling
LICENSE		LICENSE
README.md		README.md

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SAP_WGS

Whole-genome sequencing of the Sorghum Asssociation Panel

Sorghum Association Panel Whole-Genome Sequencing Establishes Cornerstone Resource for Dissecting Genomic Diversity

Analysis scripts:

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

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Whole-genome sequencing of the Sorghum Asssociation Panel

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