Yes, we support a pair of workflows that are implemented to support the discovery and annotation of human genetic variants.

The wf-human-variation workflow has been implemented for the analysis of germline genomes and uses the Clair3 method for calling of SNPs.

The Clair3 method is also used in the wf-somatic-variation workflow that may be used to call SNP variants in tumour samples that may be sequenced in combination with a paired normal sample.

While these workflows have been implemented for human use cases, they can also be used for non-human analyses when an appropriate reference genome is supplied.

For SNV variant calling in smaller (and haploid) genomes we offer a workflow, wf-bacterial-genomes, that uses the Medaka software to call variants relative to a provided reference sequence.