From 062a50c6005a5fa1da65b59b8545c7a47b014113 Mon Sep 17 00:00:00 2001
From: Jacob Pfeil <jpfeil@ucsc.edu>
Date: Sat, 25 Mar 2017 17:34:23 -0700
Subject: [PATCH] Fix check for coordinate sorted bam

---
 run_varscan | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_varscan b/run_varscan
index 6ea1143..e1a9954 100755
--- a/run_varscan
+++ b/run_varscan
@@ -131,7 +131,7 @@ fi
 
 # Check that the bam files are sorted
 issort(){
-  didsort=$(samtools view -H $1 | grep ^@HD | cut -f3)
+  didsort=$(samtools view -H $1 | grep -o 'SO:coordinate')
   if [[ "$didsort" != 'SO:coordinate' ]]; then
     graceful_death "it looks like $1 is not sorted by coordinate, please run samtools sort"
   fi