This repository includes code use in the article:

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

Building the Sorghum HapMap (/HAPMAP/Sorghum-HapMap)

SNP calling:

0_Sentieon_BWA_Batch5.sh - Sample of alignment file using BWA
1_Sentieon_merge_and_remove_duplicates.sh - Merging Bam files according to Figure S2A
2_bam_stat.sh - Calculate alignment stats
3_Sentieon_GATK_command_line_Indel_realigner.sh - Realign reads around InDels
4_Sentieon_GATK_command_line_Recal_providing_list.sh - Recalibration using high quality positions 5_Sentieon_GATK_command_line_HC_step2.sh - Haplotypes (produces gVCFs)
6_joint_variant_calling.sh - Call the variants and produce a VCF file.

Describing the Population:

Population_structure_pub.Rmd: - Calculates principal component analysis on the marker matrix using SNPrelate. Plots included
MAF_FST.Rmd - Calculates Allele frequency spectrum and FSTs between races
Duplicates - Checking the duplicates IBS matrix
Linkage_disequilibrium.Rmd - Code use to plot local LD plot and classic LD decay plots.

Misc:

Filter_MAF_OE.py - Extract monomorphic sites and sites with a threshold of heterozygosity
count_fastq.sh - Count the number of reads in a fastq
vcfaddanot.py - Add allele balancing field AB in a vcf file

Deleterious alleles: (/HAPMAP/Deleterious)

Deleterious_analysis_manuscript.Rmd - R Notebook, contains the code to analyze the Deleterious load in both maize and sorghum. Generates figure 2 of the main manuscript.

Deleterious_distribution-copy.Rmd - Code use to plot the distribution of deleterious alleles across the sorghum chromosome, it overlays population recombination rates and gene density.

Domestication-manuscript.Rmd - Analyze deleterious load in previously identified improvement and domestication genes.

DAF_maize_manuscript.Rmd - Gets the Derived Allele Frequencies from maize in the right format.

GERP_distribution.Rmd - Calculates some genome wide statistics on sorghum GERP scores.

Evolutionary model: (/HAPMAP/Evol_model)

Defining sorghum genome windows:

The midpoint distance between adjacent genes was calculated and a series of intervals that covered each chromosome from start to end were calculated. In total, the sorghum genome was divided into 34,028 fragments. Go to Sorghum-HapMap/Evol_model/Windows/ for details.

Genetic diversity (Pi):

average_pi_per_genewindow.py - Average pi per window
average_pi_per_window.bed - Output, average pi per window

Recombination rates:

FASTEPRR.R: Wrappper to calculate rho across the genome in fixed windows
FASTEPRR_segments.R: Wrapper to calculate rho across windows specified in a bed file
Recombination_Rates.Rmd: R Notebook for plotting recombination rates across the chromosomes together with gene density

GERP (Genomic evolutionary rate profiling).-

TAU (SSW 20bp alignment between sorghum and maize).-

CNN (DeepEvolution): (/HAPMAP/CNN)

Here we are including three folders with the code for the prediction of both genetic diversity and fractionation status. The input data and the output data in graphical and tabular data.

resnet_diversity_feature_importance.py - CNN for predicting nucleotide diversity
resnet_frac_feature_importance.py - CNN for predicting fractionation status

Circos Plots: (/HAPMAP/CIRCOS)

1_gene_density.py: - Calculates gene density per chromosome from a gff3 file
CIRCOS plot config files: (/HAPMAP/CIRCOS/cplot) - includes conf files (circos.conf, ideogram.conf, mycolors.conf, circos_dev.conf and ticks.conf) also includes the output in png and svg formats.
data: (/HAPMAP/CIRCOS/cplot) - data used as input

Data availability:

The raw sequencing data for the TERRA-MEPP lines is available through the NCBI BioProject PRJNA513297. Mace et al. raw data is available through the BioProject PRJNA182489, TERRA-REF raw data is available through the data commons database at CyVerse: http://datacommons.cyverse.org/browse/iplant/home/shared/terraref. Gene expression raw data is available through the Bioproject PRJNA503076. SIFT raw results and VCF files among others are available through the CyVerse repository: http://datacommons.cyverse.org/browse/iplant/home/shared/GoreLab/dataFromPubs (DOI:10.####/pending once accepted). Code used throughout the article is available at the GitHub repository: https://github.com/GoreLab/Sorghum-HapMap.