While previous recipes were focused on giving an overview of Python libraries to deal with alignment and variant call data, we concentrate on actually using them with a clear purpose in mind here.

If you are using NGS data, chances are that your most important file to analyze is a VCF file, produced by a genotype caller such as samtools mpileup, or GATK. The quality of your VCF calls may need to be assessed and filtered. Here, we will put in place a framework to filter SNP data. Rather than giving you filtering rules (an impossible task to be performed in a general way), we give you procedures to assess the quality of your data. With this, you can devise your own filters.