let mutect2 ?(configuration=Gatk.Configuration.Mutect2.default) bam_pair =
let configuration_name = configuration.Gatk.Configuration.Mutect2.name in
let configuration_json = Gatk.Configuration.Mutect2.to_json configuration in
let make_target
~run_with ~input ~result_prefix ?more_edges () =
match input with
| Variant_caller.Somatic {normal; tumor} ->
Gatk.mutect2
~configuration ?more_edges ~run_with
~input_normal_bam:normal ~input_tumor_bam:tumor
~result_prefix `Map_reduce in
somatic_variant_caller
{Variant_caller.name = "Mutect";
configuration_json;
configuration_name;
make_target;}
bam_pair