Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences

This repository consists of minisatellite VNTR genotypes for 2,800 samples (2,770 individuals). The raw VCF files were produced using VNTRseek on xxx data sources: 30 high coverage WGS datasets from the 1000 Genomes Project phase 3, 2,504 unrelated genomes from New York Genome Center (NYGC), 253 genomes from Simons Diversity Genome Project (SGDP), two tumor-normal breast cancer samples from Illumina Basespace, haploid genomes CHM1 and CHM13, and seven genomes from the Personal Genome Project from the Genome In A Bottle Consortium (GIAB). Raw VCF files are provided for each data source separately.

The raw VCF files were preprocessed (preprocess.sh) to extract genotypes and provided in VNTRseek_preprocessed_data.tar.gz (uncompressed size 10G). The R Markdown code to analyze the preprocessed data and produce figures and tables is also provided (tables_and_figures.Rmd). For more information see the ReadMe file.

This work was supported in part by NSF grants IIS-1423022 and DBI-1559829.