Add flanking sequence context to a VCF data frame — add_seq

Extracts seq_context_width bases upstream and downstream of each variant position from the reference genome and attaches them as a new column named seq.<N>bases where N = 2 * seq_context_width + 1.

Usage

add_seq_context(df, ref_genome, seq_context_width = 10, name_of_vcf = NULL)

Arguments

df: A VCF as a data frame / data.table with columns CHROM and POS.
ref_genome: A BSgenome object or a character identifier accepted by normalize_genome_arg().
seq_context_width: Number of flanking bases on each side (default 10, producing a 21-base window).
name_of_vcf: Optional VCF name used in warning/error messages.

Value

df with an added character column seq.<N>bases.