Analyzing data in the variant call format

After running a genotype caller (for example, GATK or samtools), you will have a variant call format (VCF) file reporting on genomic variations, such as single-nucleotide polymorphisms (SNPs), Insertions/Deletions (INDELs), copy number variation (CNVs), and so on. In this recipe, we will discuss VCF processing with the PyVCF module.

Getting ready

While next-generation sequencing 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 1000 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 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 Debian, Ubuntu, and...