diff --git a/dummypipeline.sh b/dummypipeline.sh
index 1b2f1337c8adeca0a1af76ef9a48bff1383ef12e..a7af9d462c981b79ffcb12cfe5cbbba7273ae47d 100644
--- a/dummypipeline.sh
+++ b/dummypipeline.sh
@@ -2,8 +2,11 @@
 # qsub/slurm/scheduler options can go here
 # Define ref
 REF=ref.fa
+# Path to known SNPS
 DBSNP=/path/to/DB/SNP.vcf
+# Path to GATK jar file
 GenomeAnalysisTK=/path/to/GATK/GenomeAnalysisTK.jar
+# Define stud name, take as variable 
 STUB=$1
 # trim data
 sickle pe -f $STUB-R1.fq.gz -r $STUB-R2.fq.gz -o $STUB-R1.fq.tr -p $STUB-R2.fq.tr -s $STUB.singles.tr -l 45 -t sanger