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From the latest 1000 genomes release, get the variant calls for chr22 in VCF format (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/).
Write a Python script which reads from the VCF all SNPs with minor allele frequency greater than 5% (note that VCF files also contain other types of variants), and computes the linkage disequilibrium between each pair.
Identify contiguous runs of linked variants (LD > 0). Produce a plot showing both the raw LD score for each adjacent pair and the linked blocks.