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