Bioinformatics with Python Cookbook - Second Edition

Getting ready

While NGS is all about big data, there is a limit to how much I can ask you to download as a dataset for this book. I believe that 2 to 20 GB of data for a tutorial is asking too much. While the 1,000 Genomes' VCF files with realistic annotations are in this order of magnitude, we will want to work with much less data here. Fortunately, the Bioinformatics community has developed tools to allow for the partial download of data. As part of the SAMtools/htslib package (http://www.htslib.org/), you can download tabix and bgzip, which will take care of data management. On the command line, perform the following:

tabix -fh ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/supporting/vcf_with_sample_level_annotation/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.vcf.gz ...