A tool to detect minority variants in HIV-1 and HCV populations

What is MinVar?

A command-line tool to discover drug resistance mutations in HIV-1 and HCV populations using deep sequencing data. Developed at IMV, UniZurich.


The report for HIV-1 includes resistance information to antiviral drugs as predicted by HIVDB.

Explore HIV-1 report

HCV report includes estimate of the genotype and the list of resistance associated substitutions (RAS) with frequency.

Explore HCV report

Designed for clinicians

Only one input file in FASTQ format is required, no need to set parameters. The final output is a PDF report with annotated mutations.


On an extensive set of control experiments, MinVar reliably called variants down to 5%. In the paper we recommend and motivate this as an accurate detection threshold.


Run time is in the order of a few minutes per sample; negligible compared to the overall experiment.


MinVar was successfully tested with reads from Illumina MiSeq and Roche/454 sequencing platforms. (HCV was tested with Illumina only).


See relevant page on documentation website.


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