let vc =
let normal =
Insane_library.(fastq_list ~dataset:(fst normal) (snd normal))
in
let tumor =
Insane_library.(fastq_list ~dataset:(fst tumor) (snd tumor))
in
let ot_hla =
normal |> Bfx.concat |> Bfx.optitype `DNA |> Bfx.to_unit
in
let align fastq =
Bfx.list_map fastq ~f:(Bfx.lambda (fun fq ->
Bfx.bwa_mem fq
~reference_build:"b37"
|> Bfx.picard_mark_duplicates
~configuration:Biokepi.Tools.Picard.Mark_duplicates_settings.default
)) in
let normal_bam = align normal |> Bfx.merge_bams in
let tumor_bam = align tumor |> Bfx.merge_bams in
let bam_pair = Bfx.pair normal_bam tumor_bam in
let indel_realigned_pair =
Bfx.gatk_indel_realigner_joint bam_pair
~configuration: Biokepi.Tools.Gatk.Configuration.default_indel_realigner
in
let final_normal_bam =
Bfx.pair_first indel_realigned_pair
|> Bfx.gatk_bqsr
~configuration: Biokepi.Tools.Gatk.Configuration.default_bqsr
in
let final_tumor_bam =
Bfx.pair_second indel_realigned_pair
|> Bfx.gatk_bqsr
~configuration: Biokepi.Tools.Gatk.Configuration.default_bqsr
in
let vcfs =
let normal, tumor = final_normal_bam, final_tumor_bam in
Bfx.list [
Bfx.mutect ~normal ~tumor ()
|> Bfx.save ~name:"Mutect VCF";
Bfx.somaticsniper ~normal ~tumor ()
|> Bfx.save ~name:"SS VCF";
Bfx.strelka ~normal ~tumor ()
|> Bfx.save ~name:"Strelka VCF";
] in
Bfx.list [
Bfx.to_unit vcfs;
ot_hla;
] |> Bfx.to_unit