Example notebook using machine learning to predict HLA type
Make sure to download the following files before running the notebook (chr6 VCF, chr6 VCF tabix index, and HLA data table):
http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HLA_types/20181129_HLA_types_full_1000_Genomes_Project_panel.txt