MinVar is a command-line tool to discover mutations conferring drug resistance in HIV-1 populations using deep sequencing data.
[user@host ~]$ minvar -f sample_file.fastq
... a few minutes later ...
[user@host ~]$ column -t -s ',' annotated_DRM.csv
gene pos mut freq category
...
RT 238 T 1.0 NNRTI
RT 250 N 0.9547 unannotated
RT 272 P 1.0 unannotated
RT 293 V 1.0 unannotated
RT 297 A 1.0 unannotated
RT 333 D 0.9384 unannotated
RT 333 E 0.0354 unannotated
RT 335 C 1.0 unannotated
protease 10 P 0.0223 Other
protease 10 Q 0.0185 Other
protease 10 S 0.0741 Other
protease 10 T 0.0468 Other
protease 10 V 0.5948 PIMinor
protease 11 L 1.0 PIMinor
protease 13 V 1.0 unannotated
protease 14 R 1.0 unannotated
protease 15 V 0.7143 unannotated
protease 20 T 1.0 PIMinor
protease 32 I 1.0 PIMajor
...
- MinVar is an opinionated software: it just takes a fastq file as input and does not ask the standard user to set any parameter at run time. Nevertheless, the experienced user/developer can easily change some of its settings in the source code.
- It has been tested on both Illumina MiSeq and Roche/454 sequencing reads.
- It uses state-of-the-art third tools to filter, recalibrate, and align reads and to call variants.
- Finally, single nucleotide variants are phased at codon level and amino acid mutations are called and annotated.
- Drug-resistance mutations are annotated according to Stanford HIV Drug Resistance Database (HIVDB).
- The annotated mutations are saved in a csv file (see example above) and also included in a report in markdown format that is finally converted to PDF.
See the official documentation.
MinVar has been introduced and validated in
Huber, Metzner et al., (2017) MinVar: A rapid and versatile tool for HIV-1
drug resistance genotyping by deep sequencing Journal of virological methods
240:7-13, doi:10.1016/j.jviromet.2016.11.008