id_indels {MixviR}

ID Indel-based Amino Acid Changes

Description

Identify amino acid changes associated with indel variation. Changes associated with SNVs are identified in separate function. Used by call_mutations() function.

Usage

id_indels(variant.calls, ref)

Arguments

variant.calls

Data frame with cols POS, REF, ALT, AF, DP. Additional columns will be ignored.

ref

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

Value

Data frame that includes amino acid calls based on indel variants observed in sample. Contains cols "POS", "REF_BASE", "GENE", "REF_CODON", "REF_AA", "GENE_AA_POS", "REF_IDENT", "REF", "ALT", "ALT_freq", "ALT_COUNT", "samp_codon", "samp_AA", "samp_identity", "DP"