Add notes to the GATKdocs as to when a particular annotation can/cannot be calculated.

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java

@@ -14,7 +14,8 @@ import java.util.List;
 
 
 /**
- * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele)
+ * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele).
+ * Note that the base quality rank sum test can not be calculated for homozygous sites.
  */
 public class BaseQualityRankSumTest extends RankSumTest {
     public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -46,7 +46,8 @@ import java.util.*;
 /**
  * Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
  * being seen on only the forward or only the reverse strand) in the reads? More bias is
- * indicative of false positive calls.
+ * indicative of false positive calls.  Note that the fisher strand test may not be
+ * calculated for certain complex indel cases or for multi-allelic sites.
  */
 public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation {
     private static final String FS = "FS";

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -52,6 +52,8 @@ import java.util.*;
 /**
  * Consistency of the site with two (and only two) segregating haplotypes. Higher scores
  * are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls.
+ * Note that the Haplotype Score is only calculated for sites with read coverage; also, for SNPs, the
+ * site must be bi-allelic.
  */
 public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation {
     private final static boolean DEBUG = false;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java

@@ -23,7 +23,8 @@ import java.util.Map;
  *
  * A continuous generalization of the Hardy-Weinberg test for disequilibrium that works
  * well with limited coverage per sample.  See the 1000 Genomes Phase I release for
- * more information.
+ * more information.  Note that the Inbreeding Coefficient will not be calculated for files
+ * with fewer than a minimum (generally 10) number of samples.
  */
 public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java

@@ -16,6 +16,7 @@ import java.util.List;
 
 /**
  * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele)
+ * Note that the mapping quality rank sum test can not be calculated for homozygous sites.
  */
 public class MappingQualityRankSumTest extends RankSumTest {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -19,7 +19,8 @@ import java.util.Map;
 /**
  * Variant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth.
  *
- * Low scores are indicative of false positive calls and artifacts.
+ * Low scores are indicative of false positive calls and artifacts.  Note that QualByDepth requires sequencing
+ * reads associated with the samples with polymorphic genotypes.
  */
 public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java

@@ -20,6 +20,7 @@ import java.util.List;
 
 /**
  * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error).
+ * Note that the read position rank sum test can not be calculated for homozygous sites.
  */
 public class ReadPosRankSumTest extends RankSumTest {