Adding small warning messages to not to feed any GVCF files to these tools

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java

@@ -92,7 +92,7 @@
  * </pre>
  *
  * <h3>Caveat</h3>
- * <p>This tool outputs no annotations by default, all annotations/groups must be specified explicitly. </p>
+ * <p>This tool outputs no annotations by default, all annotations/groups must be specified explicitly. This tool acceps VCF format files only. Using GVCF files as input may result in unexpected behavior. </p>
  *
  * <h3>Special note on RankSumTestAnnotations</h3>
  * <p>RankSumAnnotations produced by this tool are not the same as those produced by the HaplotypeCaller. Without the

src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java

@@ -41,6 +41,7 @@
  *     <li>If there are multiple variants that start at a site, it chooses one of them randomly.</li>
  *     <li>When there are overlapping indels (but with different start positions) only the first will be chosen.</li>
  *     <li>This tool works only for SNPs and for simple indels (but not for things like complex substitutions).</li>
+ *     <li>This tool works only with VCF files. Using GVCF files as input may result in unexpected behavior.</li>
  * </ul>
 
  * <h3>Input</h3>

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java

@@ -140,7 +140,7 @@
  * <h3>Additional notes</h3>
  * <ul>
  *     <li>This tool only accepts a single input variant file unlike earlier version of GATK, which accepted multiple
- *     input variant files.</li>
+ *     input variant files. Please do not provide non-genotyped GVCF files as input as it will not work properly with this tool.</li>
  *     <li>SNPs and indels must be recalibrated in separate runs, but it is not necessary to separate them into different
  * files. See the tutorial linked above for an example workflow. Note that mixed records are treated as indels.</li>
  *     <li></li>