2. snpToolkit menuΒΆ
$ 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