From fc09e84a593aaedc1a23b17f0b1d8dda2df606df Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 12 Jan 2022 11:02:37 +1100
Subject: gridss: add somatic variant filtering

---
 test-tnpair.nix  | 1 +
 tools/gridss.nix | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/test-tnpair.nix b/test-tnpair.nix
index a08f05d..e7d5d17 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -89,6 +89,7 @@ let
     gridss = gridss.callVariants { } (with tnpairResult.alignments; [ normal tumour ]);
     gridss2 = gridss.call (with tnpairResult.alignments; [ normal tumour ]);
     gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [ normal tumour ]);
+    gridssSomatic = gridss.filterSomatic { normalName = "mysample2"; } (gridss.call (with tnpairResult.alignments; [ normal tumour ]));
     "merged-shards.bam" = samtools.merge { } tnpairResult.shards;
     "merged.bam" = samtools.merge { } [ tnpairResult.alignments.tumour tnpairResult.alignments.normal ];
     "merged-namesorted.bam" = samtools.merge { } [ (nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal) ];
diff --git a/tools/gridss.nix b/tools/gridss.nix
index f52eb6e..f5b1e0e 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -100,4 +100,6 @@ rec {
   # As call but include assemblies in output
   callAndAssemble = inputs:
     gridss.annotateAndAssemble { } (map gridss.preprocessBam inputs);
+
+  filterSomatic = callBionixE ./gridss-somatic-filter.nix;
 }
-- 
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