Mutserve Variant Calling:

mutserve call
  --reference rCRS.fasta
  --output HG00096.vcf.gz
  --threads 4
  *.bam

The full list of parameters is available here.

Mutserve Variant Annotation:

mutserve annotate
  --input variantfile.txt
  --annotation rCRS_annotation_2020-08-20.txt
  --output AnnotatedVariants.txt

rCRS.fasta, rCRS_annotation_2020-08-20.txt, and rCRS_annotation_descriptions.md are available in the Mutserve2 repository ($MUTSERVE_DATA/).