From 6d5b643a9d89a5274baab4359596b38b81dfbede Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Tue, 17 May 2016 08:42:49 -0400
Subject: [PATCH] Fix tagging syntax

Syntax was given as -V:format,name but should be -V:name,format
---
 .../gatk/tools/walkers/variantutils/CombineVariants.java  | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
index f89509603..8a11da65a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
@@ -72,9 +72,9 @@ import java.util.*;
  * </ul>
  *
  * <p>By default, the input sets will be named variants, variants2, variants3, and so on. You can override this by
- * providing an explicit name tag for each input, using the syntax " -V:format,name". Each input tagged in this
+ * providing an explicit name tag for each input, using the syntax " -V:name,format". Each input tagged in this
  * way will be labeled as such in the output (i.e., set=name rather than set=variants2). For example, you could specify
- * a set of control samples as " -V:vcf,control my_control_samples.vcf", and the resulting VCF records would contain
+ * a set of control samples as " -V:control,vcf my_control_samples.vcf", and the resulting VCF records would contain
  * the annotation "set=control" in the INFO field. It is strongly recommended to provide explicit names in this way
  * when a rod priority list is provided.</p>
  *
@@ -123,8 +123,8 @@ import java.util.*;
  *
  * <h3>Caveats</h3>
  * <ul>
- * <li>This tool is not intended to manipulate GVCFS! To combine GVCF files output by HaplotypeCaller, use CombineGVCFs.</li>
- * <li>To join intermediate VCFs produced by running jobs in parallel by interval (e.g. by chromosome), use CatVariants.</li>
+ * <li>This tool is not intended to manipulate GVCFS! To combine GVCF files output for different samples by HaplotypeCaller, use CombineGVCFs.</li>
+ * <li>To join intermediate VCFs produced by running jobs in parallel by interval (e.g. by chromosome) from the same sample, use CatVariants.</li>
  * </ul>
  *
  * <h3>Additional notes</h3>