From 2bf74101a862d0417ccda2bafe55e0d2616d1e1a Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 15 Jan 2019 14:31:15 +1100
Subject: strelka: add germline calling

---
 test-tnpair.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
index c531a83..8b268ec 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -15,7 +15,7 @@ let
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
   check = fastqc.check {};
-  callVariants = strelka.call {};
+  callVariants = strelka.callSomatic {};
   markdup = samtools.markdup {};
   fixmate = samtools.fixmate {};
 
@@ -35,6 +35,7 @@ let
   processPair = { tumour, normal }: rec {
     alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
     variants = callVariants alignments;
+    glvariants = strelka.call {} (builtins.attrValues alignments);
     platypusVars = platypus.call {} (builtins.attrValues alignments);
   };
 
@@ -43,6 +44,7 @@ let
   testNaming = linkDrv [
     (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
     (ln tnpairResult.variants "strelka")
+    (ln tnpairResult.glvariants "strelka-gl")
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
     (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
-- 
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