Detecting microsatelite indels from paired BAMs By Yosi Maruvka
The loci file for hg38: gs://getzlab-workflows-reference_files-oa/hg38/msmutect/hg38_1_to_15_loci.phobos
Please checkout MSMutect_v2.0.1.sh
for the workflow logic.
More information on outputs of the workflow, please check the original MSmutect repo