In ojcharles/hivdrg: HIV Drug Resistance Genotyping

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hivdrg

overview

hivdrg is a R package to enable synonymous / non-synonymous characterisation of HIV genetic data for the PANGEA project. Also provides HIV antiviral drug resistance genotyping. Accepted inputs are FASTA (whole genomes & fragments) which will be mapped to selected reference NGS variant data assembled to a supported reference is accepted in VCF >= ver4.0 & Varscan2 tab formats.

Database

A text database extracted in July 2020 from the Stanford resistance database. Shafer RW(2006). Rationale and Uses of a Public HIV Drug-Resistance Database. Journal of Infectious Diseases 194 Suppl 1:S51-8

Installation

You can install the current version from with: GitHub

install.packages("devtools")
devtools::install_github("ojcharles/hivdrg")

Dependencies for FASTA file handling are MAFFT and SNP-Sites available preferably via conda. snp-sites >= 2.3 has been tested.

``` {bash eval = FALSE} conda config --add channels bioconda conda install snp-sites conda install mafft

## Usage - resistance genotyping

note: there are 5 supported variants in hivdrg, vcf and tab files must be assembled against one of these. fasta files will be aligned to the chosen reference and variants called.

```r
library("hivdrg")

# select a fasta, vcf, or varscan tab file
my_sample = system.file("testdata", "example.vcf", package = "hivdrg")

# hivdrg provides the following function to return a table of annotated variants
data = call_resistance(infile = my_sample, all_mutations = F, ref = 5)


head(data[,c("GENEID","aachange", "freq", "phenotype")])

Usage - synonymous / non-synonymous characterisation

## call all variants

mutations_all = call_resistance(infile = my_sample, all_mutations = T,ref = 5)


# are there any non-synonymous (DNA variants that result in a change of amino acid) variants in resistance genes
mutations_nonsyn = mutations_all[mutations_all$CONSEQUENCE == "nonsynonymous",]


# here the top 3 mutations are nonsynonymous, with no identified resistance effect.
head(mutations_nonsyn[,c("GENEID","aachange", "freq", "CONSEQUENCE","phenotype")])

Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on the GitHub Issues page. For questions and other discussions feel free to contact. Oscar Charles - Developer

ojcharles/hivdrg documentation built on Feb. 12, 2022, 12:10 p.m.