From 2c706aaad54aeec0f224ab7c313ac22aebe0bb9e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 26 Oct 2018 08:05:28 +1100
Subject: init: mutect

---
 tools/mutect-call.nix | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 tools/mutect-call.nix

(limited to 'tools/mutect-call.nix')

diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix
new file mode 100644
index 0000000..9fd009b
--- /dev/null
+++ b/tools/mutect-call.nix
@@ -0,0 +1,42 @@
+{bionix
+, nixpkgs
+, cosmic
+, dbsnp}:
+
+with nixpkgs;
+with lib;
+
+let
+  inherit (bionix.types) matchFiletype;
+  getVCFref = matchFiletype "mutect-call" {vcf = {ref}: ref;};
+  getBAMref = matchFiletype "mutect-call" {bam = {ref, ...}: ref;};
+  refs = map getVCFref [ cosmic dbsnp ];
+  ref = head refs;
+in
+
+assert (length (unique refs) == 1);
+
+{normal, tumour}:
+
+assert (ref == getBAMref normal && ref == getBAMref tumour);
+
+stdenv.mkDerivation {
+  name = "mutect";
+  buildInputs = [ bionix.mutect.app ];
+  buildCommand = ''
+    ln -s ${normal} normal.bam
+    ln -s ${tumour} tumour.bam
+    ln -s ${dbsnp} dbsnp.vcf
+    ln -s ${cosmic} cosmic.vcf
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx {} ref} ref.fa.fai
+    ln -s ${bionix.samtools.dict {} ref} ref.dict
+    mutect --analysis_type MuTect \
+      --reference_sequence ref.fa \
+      --cosmic cosmic.vcf \
+      --dbsnp dbsnp.vcf \
+      --input_file:normal normal.bam \
+      --input_file:tumour tumour.bam \
+      --out $out
+  '';
+}
-- 
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