diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 6cab6d95f..312b505ec 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/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 getKeyNames() { return Arrays.asList("BaseQRankSum"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 2d1d1978c..c4025a25c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/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"; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 803bf514c..94b0636f4 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java index a14007147..8728e5aa4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +++ b/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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 157c615d7..9857c339f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index ffc852903..b942d9817 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/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 { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 27a9306d4..d762af428 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/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 {