From 8073a713111095a48bec6a830de80c1529426fd2 Mon Sep 17 00:00:00 2001
From: Arun Seetharam <arnstrm@iastate.edu>
Date: Tue, 21 Feb 2017 09:17:11 -0600
Subject: [PATCH] added run gsnap script

---
 runGSNAP.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 runGSNAP.sh

diff --git a/runGSNAP.sh b/runGSNAP.sh
new file mode 100644
index 0000000..6a22d7c
--- /dev/null
+++ b/runGSNAP.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+GMAPDB="/work/GIF/arnstrm/GENOMEDB"
+DB_NAME="Gmax_275_v2.0_gsnap"
+R1="$1"
+R2="$2"
+OUTFILE=$(basename ${R1} |cut -f 1 -d "_")
+gsnap \
+   -d ${DB_NAME} \
+   -D ${GMAPDB}
+   -t 16 \
+   -B 5 \
+   -N 1
+   -m 5 \
+   --gunzip \
+   --fails-as-input \
+   --input-buffer-size=10000000 \
+   --output-buffer-size=10000000 \
+   -A_gsnap.sam  ${R1} ${R2} > ${OUTFILE}_gsnap_gsnap.sam
\ No newline at end of file