2. snpToolkit menu

$ snptoolkit -h
 usage: snptoolkit [-h] {explore,annotate,combine,viz,analyse} ...

     snpToolkit can takes vcf files, as well as bam files (optional) as inputs. The vcf files could be generated using samtools/bcftools, gatk HaplotypeCaller or freeBayes.
     Please visit https://snptoolkit.readthedocs.io/en/latest/index.html for more information.


 positional arguments:
   {explore,annotate,combine,viz,analyse}
                         commands
     explore             Explore your vcf files before annotation
     annotate            Annotate one or multiple vcf files
     combine             Identify polymorphic sites and create distribution table and alignment file in fasta format
     viz                 visualize snptoolkit output files
     analyse             analyse your SNPs data

 optional arguments:
   -h, --help            show this help message and exit