snptoolkit 2.3.0

Explore, filter, annotate and analyse your SNPs/indels from VCF files

Please visit the full documentation at https://snptoolkit.readthedocs.io/en/latest/index.html

snpToolkit is a computational framework written in Python 3. snpToolkit allows users to: - Visualize the content of their VCF files. - Filter SNPs based on multiple criteria. - Extract the distribution of all indels according to genome annotation. - Visualize and explore the annotated SNPs for all analyzed files. - Combine all snpToolkit output files generated using the annotate option. - Analyse your data using two dimentionality reduction methods: PCA and UMAP. snpToolkit detects automatically if the input vcf files were generated using samtools mpileup, gatk HaplotypeCaller or freebayes. Vcf files could be gzipped or not.