Selecting and classifying variants with VariantAnnotation

In pipelines where we've called variants, we'll often want to do subsequent analysis steps that need further filtering or classification based on features of the individual variants, such as the depth of coverage in the alternative allele. This is best done from a VCF file, and a common protocol is to save a VCF of all variants from the actual calling step and then experiment with filtering that. In this section, we'll look at taking an input VCF and filtering it to retain variants in which the alternative allele is the major allele in the sample.

Getting ready

We'll need a tabix index VCF file; I provide one in the datasets/ch2/sample.vcf.gz file...