From 4188745074ef56981867428c2307d25ca9159124 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Tue, 21 Mar 2017 12:55:30 -0400
Subject: [PATCH] Document how VTT orders samples in output table

---
 .../tools/walkers/variantutils/VariantsToTable.java    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
index ef4546181..5a4b7e2b5 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
@@ -69,12 +69,10 @@ import java.util.*;
  * </p>
  *
  * <h3>Input</h3>
- * <p>
  * <ul>
  *     <li>A VCF file</li>
  *     <li>A list of -F fields to write</li>
  * </ul>
- * </p>
  *
  * <h3>Output</h3>
  * <p>
@@ -98,9 +96,11 @@ import java.util.*;
  *     et cetera...
  * </pre>
  *
- * <h3>Caveat</h3>
- * <p>If a VCF record is missing a value, then the tool by default throws an error, but the special value NA can
- * be emitted instead if requested at the command line using --allowMissingData.</p>
+ * <h3>Caveats</h3>
+ * <ul>
+ *     <li>Some annotations cannot be applied to all variant sites, so VCFs typically contain records where some annotation values are missing. By default this tool throws an error if you request export of an annotation for which not all records have values. You can override this behavior by setting --allowMissingData in the command line. As a result, the tool will emit the special value NA for the missing annotations in those records.</li>
+ *     <li>When you request export of sample-level annotations (FORMAT field annotations such as GT), the annotations will be identified per-sample. If multiple samples are present in the VCF, the columns will be ordered alphabetically by sample name (SM tag).</li>
+ * </ul>
  *
  * @author Mark DePristo
  * @since 2010