- * If a BAM file contains erroneous or missing mapping qualities, this 'filter' will set - * all your mapping qualities to a given value. Default being 60. + * If a BAM file contains erroneous or missing mapping qualities (MAPQ), this read transformer will set all your + * mapping qualities to a given value (see arguments list for default value). *
* + *ReassignOneMappingQualityFilter: reassigns a single MAPQ value, as opposed to all those found in the BAM file.
+ * + *Note that due to the order of operations involved in applying filters, it is possible that other read filters + * (determined either at command-line or internally by the tool you are using) will be applied to your data before + * this read transformation can be applied. If one of those other filters acts on the read mapping quality (MAPQ), + * then you may not obtain the expected results. Unfortunately it is currently not possible to change the order of + * operations from command line. To avoid the problem, we recommend applying this filter separately from any other + * analysis, using PrintReads.
+ * * *@@ -50,9 +63,9 @@ import org.broadinstitute.sting.commandline.Argument; * *
- * java - * -jar GenomeAnalysisTK.jar - * -rf ReassignMappingQuality + * java -jar GenomeAnalysisTK.jar \ + * -T PrintReads \ + * -rf ReassignMappingQuality \ * -DMQ 35 ** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java index f31313a86..232b7ed3d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.Argument; * A read filter (transformer) that changes a given read mapping quality to a different value. * *
- * This 'filter' will change a certain read mapping quality to a different value without affecting reads that + * This read transformer will change a certain read mapping quality to a different value without affecting reads that * have other mapping qualities. This is intended primarily for users of RNA-Seq data handling programs such * as TopHat, which use MAPQ = 255 to designate uniquely aligned reads. According to convention, 255 normally * designates "unknown" quality, and most GATK tools automatically ignore such reads. By reassigning a different @@ -46,7 +46,6 @@ import org.broadinstitute.sting.commandline.Argument; * that have no assigned mapping qualities. *
* - * ** BAM file(s) @@ -60,8 +59,8 @@ import org.broadinstitute.sting.commandline.Argument; * *
- * java - * -jar GenomeAnalysisTK.jar + * java -jar GenomeAnalysisTK.jar + * -T PrintReads * -rf ReassignOneMappingQuality * -RMQF 255 * -RMQT 60 diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index 6e7bc9805..87323cf87 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -46,7 +46,12 @@ import java.util.Map; /** - * The allele balance (fraction of ref bases over ref + alt bases) across all biallelic het-called samples + * Allele balance across all samples + * + *The allele balance is the fraction of ref bases over ref + alt bases.
+ * + *Caveats
+ *Note that this annotation will only work properly for biallelic samples that are called as heterozygous.
*/ public class AlleleBalance extends InfoFieldAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index 608257b54..f5930078f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -51,7 +51,7 @@ import java.util.List; *The allele balance is the fraction of ref bases over ref + alt bases.
* *Caveats
- *Note that this annotation will only work properly for biallelic het-called samples.
+ *Note that this annotation will only work properly for biallelic samples that are called as heterozygous.
*This is an experimental annotation. As such, it is unsupported; we do not make any guarantees that it will work properly, and you use it at your own risk.
*/ public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {