Analyzing data in VCF

After running a genotype caller (for example, GATK or SAMtools), you will have a VCF file reporting on genomic variations, such as SNPs, insertions/deletions (INDELs), copy number variations (CNVs), and so on. In this recipe, we will discuss VCF processing with the PyVCF module.

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...