From fb16ae15f41a81b8f60fae829400afd987dbff9a Mon Sep 17 00:00:00 2001
From: Steve Huang <shuang@broadinstitute.org>
Date: Mon, 22 Apr 2019 17:54:11 -0400
Subject: [PATCH] update usage example for CreateHadoopBamSplittingIndex
 (#5898)

---
 .../tools/spark/CreateHadoopBamSplittingIndex.java       | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndex.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndex.java
index 5942b209d5f..1b33bbac337 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndex.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndex.java
@@ -42,7 +42,14 @@
  * <pre>
  *     gatk CreateHadoopBamSplittingIndex \
  *         -I input_reads.bam \
- *         -O input_reads.bam.splitting-bai
+ *         -O input_reads.bam.sbi
+ * </pre>
+ * or if one wants to generate bai as well
+ * <pre>
+ *     gatk CreateHadoopBamSplittingIndex \
+ *         -I input_reads.bam \
+ *         -O input_reads.bam.sbi \
+ *         --create-bai
  * </pre>
  */
 @CommandLineProgramProperties(summary = "Create a Hadoop BAM splitting index and optionally a BAM index from a BAM file",