snpeff_vcf: Nucleotide variants in example genome samples with snpeff...
In prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies

An example dataset containing 14 variants from 49 genome samples that has been annotated using snpeff.

1	snpeff_vcf

vcfR class object with three sections:

meta: The metadata for the VCF file including the file format version number
fix: A character matrix with 14 rows and 8 columns. Contains information on chromosome (CHROM), genome position (POS), reference genome allele (REF), and alternative allele (ALT). Information column (INFO) contains a field called "ANN" which provides the snpeff annotation including predicted functional impact of the variant on the protein function.
gt: A character matrix with 14 rows and 49 columns. Presence/absence for each variant defined in fix. Colnames are sample IDs.