add_depths_to_ref {MixviR}

Add Read Depths To Ref

Description

Add column of total read depths for a given sample to reference df. Run as part of id_mutations().

Usage

add_depths_to_ref(ref, samp.variants)

Arguments

ref

reference genome in "MixVir" format (from create_ref() function)

samp.variants

Data frame produced by function vcf_to_mixvir(). Contains columns "CHR", "POS", "REF", "ALT", "DP", "ALT_COUNT".

Value

Original 'ref' data frame with depth (DP) column added: cols "genomic_pos" "ref_base" "gene" "ref_codon" "ref_AA" "GENE_AA_POS" "ref_identity" "DP"