From b2b9a3be4e8544f569cf6155b8a34f405d4a2591 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 25 Sep 2019 15:26:34 +1000
Subject: facets: assume sorted vcf

---
 tools/facets-call.nix | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

(limited to 'tools')

diff --git a/tools/facets-call.nix b/tools/facets-call.nix
index 021cacc..a736627 100644
--- a/tools/facets-call.nix
+++ b/tools/facets-call.nix
@@ -14,11 +14,6 @@ stage {
   name = "facets";
   buildInputs = [ facets.app ];
   buildCommand = ''
-    # Facets requires lexical sorting on the VCF files
-    grep '^#' ${vcf} > input.vcf
-    grep -v '^#' ${vcf} | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n >> input.vcf || true
-
-    # Now actually run facets
-    snp-pileup input.vcf $out ${concatStringsSep " " bams}
+    snp-pileup ${vcf} $out ${concatStringsSep " " bams}
   '';
 }
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