call_resistance: HIV Resistance Genotyping from command line
In ojcharles/hivdrg: HIV Drug Resistance Genotyping

Description Usage Arguments Value

View source: R/call_resistance.R

Command line version of the website application Takes as input a VCF, varscan tab or fasta file. The program assumes variant files are generated relative to Merlin strain. Fasta files if not Whole Genome, or not aligned / assembled relative to Merlin are Processed using MAFFT & snp-sites. In this case the output files are returned to your working directory.

call_resistance(
  infile = system.file("testdata", "example.vcf", package = "hivdrg"),
  all_mutations = TRUE,
  ref = 5,
  outdir = ""
)

`infile`	the input fasta, vcf or varscan.tab file
`all_mutations`	when FALSE only recognised resistant variants present are returned.
`ref`	a choice of 5 HIV representative genomes, pass a number 1-5, "AG_L39106.1","C_AF067155.1","G_U88826.1", "JX239390.1","K03455.1"
`outdir`	for fasta input files intermediate alignment fasta & vcf files are generated, this defines the directory they are saved to. "out.fasta" "out.vcf"