split SV and indel calling into its own command and create an all-in-one run command for users starting from scratch.
split SV and indel calling into its own command and create an all-in-one run command for users starting from scratch.

EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller