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Another possibility is to use glactools. I will show this by using data from the 1000 genomes. First, we download the chromosome names and length for the reference: wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.fai We then require information on the panels from the VCF file: wget https://personal.broadinstitute....


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