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(+)
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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