From a5c144db4d23eb2190ef84b60b063918d6026712 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 13 Nov 2014 12:53:29 -0500
Subject: [PATCH] added scripts to generate hs38a.fa and hs38d6.fa

---
 extras/{run-HLA.sh => run-HLA} | 0
 extras/run-gen-hs38a           | 9 +++++++++
 extras/run-gen-hs38d6          | 9 +++++++++
 3 files changed, 18 insertions(+)
 rename extras/{run-HLA.sh => run-HLA} (100%)
 create mode 100755 extras/run-gen-hs38a
 create mode 100755 extras/run-gen-hs38d6

diff --git a/extras/run-HLA.sh b/extras/run-HLA
similarity index 100%
rename from extras/run-HLA.sh
rename to extras/run-HLA
diff --git a/extras/run-gen-hs38a b/extras/run-gen-hs38a
new file mode 100755
index 0000000..cd119ad
--- /dev/null
+++ b/extras/run-gen-hs38a
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+root=`dirname $0`
+
+wget -O- ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz \
+  | gzip -dc > hs38a.fa
+
+[ ! -f hs38a.fa.alt ] && grep _alt $root/resource-GRCh38/hs38d6.fa.alt > hs38a.fa.alt
+[ ! -f hs38a.fa.bwt ] && echo -e "\nPlease run 'bwa index hs38a.fa'...\n"
diff --git a/extras/run-gen-hs38d6 b/extras/run-gen-hs38d6
new file mode 100755
index 0000000..86d6fa2
--- /dev/null
+++ b/extras/run-gen-hs38d6
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+root=`dirname $0`
+
+(wget -O- ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz \
+  | gzip -dc; cat $root/data/hs38d6-extra.fa) > hs38d6.fa
+
+[ ! -f hs38d6.fa.alt ] && cp $root/resource-GRCh38/hs38d6.fa.alt .
+[ ! -f hs38d6.fa.bwt ] && echo -e "\nPlease run 'bwa index hs38d6.fa'...\n"