diff --git a/.gitignore b/.gitignore
new file mode 100644
index 000000000..be613e7d6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,17 @@
+/*.bam
+/*.bai
+/*.bed
+*.idx
+*~
+/*.vcf
+/*.txt
+/*.csh
+/.*
+/*.pdf
+/*.eval
+*.ipr
+*.iws
+queueScatterGather
+/foo*
+/bar*
+integrationtests/