MinVar relies on the following libraries with their own specific licenses:
- pandas (library for data analysis) simplified BSD licence
- Biopython (library for biological computation), distributed under Biopython licence
The following external tools are called by the program:
- BLAST (sequence alignment), code distributed in lesser GPL
- samtools (sequence manipulation), MIT licence
- GATK (base quality recalibration), commercial licence (see below)
- picard-tools (sequence manipulation), only used together with GATK, MIT licence
- bwa (sequence alignment), GPL v3 licence
- seqtk (sequence filtering), MIT licence
- lofreq (variant calling), MIT licence
Using recalibration in a commercial setting
It is worth noting that recalibration is done by GATK, which is itself subject to a dual purpose licensing: free for academic non-commercial research activities, subject to a fee for commercial use.
Starting from v1.2, MinVar by defaults does not recalibrate the base quality scores (you can evaluate the difference in this Note on recalibration). If you decide to use MinVar with recalibration for commercial purposes, you will have to obtain a licence for GATK from Broad Institute.