From 6b2486a3fe56a2c4f8b355e696f152a2d1037abe Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 25 Sep 2019 15:35:23 +1000
Subject: grch37: add dbsnp

---
 lib/references.nix | 12 ++++++++++++
 1 file changed, 12 insertions(+)

(limited to 'lib')

diff --git a/lib/references.nix b/lib/references.nix
index 7f754d6..f328bb9 100644
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -15,6 +15,18 @@ rec {
       buildCommand = "gunzip < $src > $out";
       passthru.filetype = filetype.fa {};
     };
+    dbsnp = stage {
+      name = "dbsnp-b151_GRCh37p13";
+      src = pkgs.fetchurl {
+        url = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/common_all_20180423.vcf.gz";
+        sha256 = "0jf71h5wy82xhgsjkvp05mj2grjrjlnswmr0wz4lb87g3ip3c2mm";
+      };
+      buildInputs = with pkgs; [ gawk ];
+      buildCommand = ''
+      gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
+        '';
+        passthru.filetype = filetype.vcf { ref = seq; };
+      };
     ensembl = let version = "74"; in {
       cdna = stage {
         name = "ensembl-grch37-cdna-${version}";
-- 
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