CowpeaDiversityGeneticData

The accompanying workflow and data of the global cowpea diversity analysis are found in the GitHub repository: https://github.com/SofiePearson/CowpeaDiversity

The following genetic data are included in this dataset:

RAW DATASET
"DCpea24-9409_MarkerHet0.4_raw.vcf"
The filtered dataset consisting of 10,618 accessions and 4,290 high-quality SNPs, denoted the “raw dataset” in a variant call format (VCF) file.

CULTIVATED DATASET
Two file types containing 10,617 accessions and 3,073 SNPs, filtered for minor allele frequency (MAF) at 0.01, denoted the "cultivated dataset" in VCF and raw file formats:
"DCpea24-9409_MarkerHet0.4_10617_CC_MAF0.01.vcf"
"DCpea24-9409_MarkerHet0.4_10617_CC_MAF0.01_raw.raw"
The raw file was used as input for PCA and GRM heatmap containing 10,617 accessions and 3,073 SNPs.

CULTIVATED-PRUNED DATASET
Two file types containing 10,617 accessions and 2,302 SNPs, linkage disequilibrium (LD) pruned:
"DCpea24-9409_MarkerHet0.4_10617_CC_MAF0.01_LD_pruned.vcf"
"pruneddata.bed"
"pruneddata.bim"
"pruneddata.fam"
Note PLINK format contains all three files with the pre-fix: "pruneddata", and must be kept in the same directory

NON-REDUNDANT DATASET
One file containing 9,609 accessions and 3,083 SNPs that are not LD pruned but filtered for a MAF of 0.01. Used as input for diversity analyses:
CC_9609_MAF.raw

NON-REDUNDANT PRUNED DATASET
Five files containing 9,609 accessions and 2,312 SNPs that are LD pruned:
DCpea24-9409_MarkerHet0.4_10617_CC_9609_MAF0.01_LD_pruned.vcf
pruneddata2.bed
pruneddata2.bim
pruneddata2.fam
pruneddata_LD_9609.raw
"pruneddata2" PLINK files are used for ADMIXTURE and IBD analyses, and "pruneddata_LD_9609.raw" file is used for sNMF analysis.

NON-REDUNDANT PRUNED DATASET CONTAINING OUTGROUP
DCpea24-9409_MarkerHet0.4_2312_9610.vcf
LD pruned dataset containing 9,610 accessions (including the outgroup) and 2,312 LD pruned markers.