diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 0ac337038..f4622fa30 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -149,7 +149,7 @@ import java.util.*;
*
* Output
*
- * VCF file with raw, unrecalibrated SNP and indel calls.
+ * VCF file with raw, unfiltered SNP and indel calls. These must be filtered either by variant recalibration (best) or hard-filtering before use in downstream analyses.
*
*
* Examples
@@ -200,7 +200,6 @@ import java.util.*;
* -T HaplotypeCaller
* -R reference/human_g1k_v37.fasta
* -I sample1.bam \
- * -recoverDanglingHeads \
* -dontUseSoftClippedBases \
* [--dbsnp dbSNP.vcf] \
* -stand_call_conf 20 \
@@ -211,17 +210,12 @@ import java.util.*;
*
* Caveats
*
- * - Currently the -ploidy parameter only support the default 2 (diploid). Eventually it will be possible to change
- * its value in order to analyze data from non-diploid organisms.
* - We have not yet fully tested the interaction between the GVCF-based calling or the multisample calling and the
- * RNAseq-specific functionalities.
- * Use those in combination at your own risk.
+ * RNAseq-specific functionalities.Use those in combination at your own risk.
* - Many users have reported issues running HaplotypeCaller with the -nct argument, so we recommend using Queue to
* parallelize HaplotypeCaller instead of multithreading.
*
*
- * @author rpoplin
- * @since 8/22/11
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@@ -252,7 +246,10 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
@Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="how to solve heterogeneous kmer situations using the fast method",required=false)
protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution = HeterogeneousKmerSizeResolution.COMBO_MIN;
- @Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false, defaultToStdout = false)
+ /**
+ * This argument is meant for debugging and is not immediately useful for normal analysis use.
+ */
+ @Output(fullName="graphOutput", shortName="graph", doc="Write debug assembly graph information to this file", required = false, defaultToStdout = false)
protected PrintStream graphWriter = null;
/**
@@ -286,24 +283,26 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
private HaplotypeBAMWriter haplotypeBAMWriter;
/**
- * The type of BAM output we want to see.
+ * The type of BAM output we want to see. This determines whether HC will write out all of the haplotypes it
+ * considered (top 128 max) or just the ones that were selected as alleles and assigned to samples.
*/
@Advanced
- @Argument(fullName="bamWriterType", shortName="bamWriterType", doc="How should haplotypes be written to the BAM?", required = false)
+ @Argument(fullName="bamWriterType", shortName="bamWriterType", doc="Which haplotypes should be written to the BAM?", required = false)
public HaplotypeBAMWriter.Type bamWriterType = HaplotypeBAMWriter.Type.CALLED_HAPLOTYPES;
/**
- * If set, certain "early exit" optimizations in HaplotypeCaller will be disabled. This is most likely to be useful if
- * you're using the -bamout argument to examine the placement of reads following reassembly and are interested in the
- * reads in regions with no variations. The -forceActive and -dontTrimActiveRegions arguments may also be necessary.
+ * If set, certain "early exit" optimizations in HaplotypeCaller, which aim to save compute and time by skipping
+ * calculations if an ActiveRegion is determined to contain no variants, will be disabled. This is most likely to be useful if
+ * you're using the -bamout argument to examine the placement of reads following reassembly and are interested in seeing the mapping of
+ * reads in regions with no variations. Setting the -forceActive and -dontTrimActiveRegions flags may also be necessary.
*/
@Advanced
- @Argument(fullName = "disableOptimizations", shortName="disableOptimizations", doc="Should HaplotypeCaller skip expensive calculations in active regions with no variants?",
+ @Argument(fullName = "disableOptimizations", shortName="disableOptimizations", doc="Don't skip calculations in ActiveRegions with no variants",
required = false)
private boolean disableOptimizations = false;
/**
- * rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
+ * rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
* dbSNP is not used in any way for the calculations themselves.
*/
@ArgumentCollection
@@ -320,9 +319,8 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
/**
* If a call overlaps with a record from the provided comp track, the INFO field will be annotated
- * as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field).
- * Records that are filtered in the comp track will be ignored.
- * Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
+ * as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are
+ * filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
*/
@Advanced
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
@@ -335,58 +333,86 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
public boolean alwaysAppendDbsnpId() { return false; }
/**
- * Which annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available annotations.
+ * Which annotations to add to the output VCF file. The single value 'none' removes the default annotations. See the VariantAnnotator -list argument to view available annotations.
*/
@Advanced
- @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls. The single value 'none' removes the default annotations", required=false)
+ @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"ClippingRankSumTest", "DepthPerSampleHC"}));
/**
* Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the -A or -G arguments,
- * so annotations will be excluded even if they are explicitly included with the other options.
+ * so these annotations will be excluded even if they are explicitly included with the other options.
*/
@Advanced
@Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
protected List annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator"}));
/**
- * Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
+ * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
+ * the VariantAnnotator -list argument to view available groups. Note that this usage is not recommended because
+ * it obscures the specific requirements of individual annotations. Any requirements that are not met (e.g. failing
+ * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
*/
- @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls. The single value 'none' removes the default group", required=false)
+ @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
protected String[] annotationClassesToUse = { "Standard" };
@ArgumentCollection
private HaplotypeCallerArgumentCollection SCAC = new HaplotypeCallerArgumentCollection();
- @Argument(fullName="sample_name", shortName = "sn", doc="Name of single sample to use from a multi-sample bam. The name is case-sensitive", required=false)
+ /**
+ * You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
+ * is especially useful if your samples are all in the same file but you need to run them individually through HC
+ * in -ERC GVC mode (which is the recommended usage). Note that the name is case-sensitive.
+ */
+ @Argument(fullName="sample_name", shortName = "sn", doc="Name of single sample to use from a multi-sample bam", required=false)
protected String sampleNameToUse = null;
// -----------------------------------------------------------------------------------------------
// arguments to control internal behavior of the read threading assembler
// -----------------------------------------------------------------------------------------------
+ /**
+ * Multiple kmer sizes can be specified, using e.g. `-kmerSize 10 -kmerSize 25`.
+ */
@Advanced
@Argument(fullName="kmerSize", shortName="kmerSize", doc="Kmer size to use in the read threading assembler", required = false)
protected List kmerSizes = Arrays.asList(10, 25);
+ /**
+ * When graph cycles are detected, the normal behavior is to increase kmer sizes iteratively until the cycles are
+ * resolved. Disabling this behavior may cause the program to give up on assembling the ActiveRegion.
+ */
@Advanced
- @Argument(fullName="dontIncreaseKmerSizesForCycles", shortName="dontIncreaseKmerSizesForCycles", doc="Should we disable the iterating over kmer sizes when graph cycles are detected?", required = false)
+ @Argument(fullName="dontIncreaseKmerSizesForCycles", shortName="dontIncreaseKmerSizesForCycles", doc="Disable iterating over kmer sizes when graph cycles are detected", required = false)
protected boolean dontIncreaseKmerSizesForCycles = false;
+ /**
+ * By default, the program does not allow processing of reference sections that contain non-unique kmers. Disabling
+ * this check may cause problems in the assembly graph.
+ */
@Advanced
- @Argument(fullName="allowNonUniqueKmersInRef", shortName="allowNonUniqueKmersInRef", doc="Should we allow graphs which have non-unique kmers in the reference?", required = false)
+ @Argument(fullName="allowNonUniqueKmersInRef", shortName="allowNonUniqueKmersInRef", doc="Allow graphs that have non-unique kmers in the reference", required = false)
protected boolean allowNonUniqueKmersInRef = false;
+ /**
+ * If fewer samples than the specified number pass the minPruning threshold for a given path, that path will be eliminated from the graph.
+ */
@Advanced
- @Argument(fullName="numPruningSamples", shortName="numPruningSamples", doc="The number of samples that must pass the minPuning factor in order for the path to be kept", required = false)
+ @Argument(fullName="numPruningSamples", shortName="numPruningSamples", doc="Number of samples that must pass the minPruning threshold", required = false)
protected int numPruningSamples = 1;
+ /**
+ * As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior. See GATK 3.3 release notes for more details.
+ */
@Deprecated
- @Argument(fullName="recoverDanglingHeads", shortName="recoverDanglingHeads", doc="This argument is no longer needed as it is now the default behavior", required = false)
+ @Argument(fullName="recoverDanglingHeads", shortName="recoverDanglingHeads", doc="This argument is deprecated since version 3.3", required = false)
protected boolean DEPRECATED_RecoverDanglingHeads = false;
+ /**
+ * By default, the read threading assembler will attempt to recover dangling heads and tails. See the `minDanglingBranchLength` argument documentation for more details.
+ */
@Hidden
- @Argument(fullName="doNotRecoverDanglingBranches", shortName="doNotRecoverDanglingBranches", doc="Should we disable dangling head and tail recovery in the read threading assembler?", required = false)
+ @Argument(fullName="doNotRecoverDanglingBranches", shortName="doNotRecoverDanglingBranches", doc="Disable dangling head and tail recovery", required = false)
protected boolean doNotRecoverDanglingBranches = false;
/**
@@ -395,11 +421,15 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
* try to rescue it. A smaller number here will lead to higher sensitivity to real variation but also to a higher number of false positives.
*/
@Advanced
- @Argument(fullName="minDanglingBranchLength", shortName="minDanglingBranchLength", doc="Minimum length of a dangling branch to attempt recovery in the read threading assembler", required = false)
+ @Argument(fullName="minDanglingBranchLength", shortName="minDanglingBranchLength", doc="Minimum length of a dangling branch to attempt recovery", required = false)
protected int minDanglingBranchLength = 4;
+ /**
+ * This argument is specifically intended for 1000G consensus analysis mode. Setting this flag will inject all
+ * provided alleles to the assembly graph but will not forcibly genotype all of them.
+ */
@Advanced
- @Argument(fullName="consensus", shortName="consensus", doc="In 1000G consensus mode. Inject all provided alleles to the assembly graph but don't forcibly genotype all of them.", required = false)
+ @Argument(fullName="consensus", shortName="consensus", doc="1000G consensus mode", required = false)
protected boolean consensusMode = false;
// -----------------------------------------------------------------------------------------------
@@ -408,33 +438,16 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
/**
- * The GQ partition intervals
+ * When HC is run in reference confidence mode with banding compression enabled (-ERC GVCF), homozygous-reference
+ * sites are compressed into bands of similar genotype quality (GQ) that are emitted as a single VCF record. See
+ * the FAQ documentation for more details about the GVCF format.
*
- * Should be a non-empty list of boundaries. For example, suppose this variable is
- *
- * [A, B, C]
- *
- * We would partition our hom-ref sites into the following bands:
- *
- * X < A
- * A <= X < B
- * B <= X < C
- * X >= C
- *
- * For example, specifying bands as (1, 10, 20, 30, 40, 50) give the following GQ blocks:
- *
- * [0, 0]
- * (0, 10]
- * (10, 20]
- * (20, 30]
- * (30, 40]
- * (40, 50]
- * (50, 99]
- *
- * Note that in the GATK GQ values are capped at 99.
+ * This argument allows you to set the GQ boundaries. HC expects a list of multiple GQ threshold values. To pass
+ * multiple values, you provide them one by one with the argument, as in `-GQB 10 -GQB 20 -GQB 30` and so on. Note
+ * that GQ values are capped at 99 in the GATK.
*/
@Advanced
- @Argument(fullName="GVCFGQBands", shortName="GQB", doc="Emit experimental reference confidence scores", required = false)
+ @Argument(fullName="GVCFGQBands", shortName="GQB", doc="GQ thresholds for reference confidence bands", required = false)
protected List GVCFGQBands = new ArrayList(70) {{
for (int i=1; i<=60; ++i) add(i);
add(70); add(80); add(90); add(99);
@@ -456,20 +469,22 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
// -----------------------------------------------------------------------------------------------
/**
- * The minimum confidence needed for a given base for it to be used in variant calling.
+ * Bases with a quality below this threshold will not be used for calling.
*/
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
public byte MIN_BASE_QUALTY_SCORE = 10;
/**
- * Users should be aware that this argument can really affect the results of the variant calling and should exercise caution.
- * Using a prune factor of 1 (or below) will prevent any pruning from the graph which is generally not ideal; it can make the
+ * Paths with fewer supporting kmers than the specified threshold will be pruned from the graph.
+ *
+ * Be aware that this argument can dramatically affect the results of variant calling and should only be used with great caution.
+ * Using a prune factor of 1 (or below) will prevent any pruning from the graph, which is generally not ideal; it can make the
* calling much slower and even less accurate (because it can prevent effective merging of "tails" in the graph). Higher values
* tend to make the calling much faster, but also lowers the sensitivity of the results (because it ultimately requires higher
* depth to produce calls).
*/
@Advanced
- @Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with < X supporting kmers are pruned from the graph", required = false)
+ @Argument(fullName="minPruning", shortName="minPruning", doc = "Minimum support to not prune paths in the graph", required = false)
protected int MIN_PRUNE_FACTOR = 2;
@Advanced
@@ -477,18 +492,18 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
protected int gcpHMM = 10;
/**
- * If this flag is provided, the haplotype caller will include unmapped reads in the assembly and calling
+ * If this flag is provided, the haplotype caller will include unmapped reads (that have chromosomal coordinates) in the assembly and calling
* when these reads occur in the region being analyzed. Typically, for paired end analyses, one pair of the
* read can map, but if its pair is too divergent then it may be unmapped and placed next to its mate, taking
* the mates contig and alignment start. If this flag is provided the haplotype caller will see such reads,
* and may make use of them in assembly and calling, where possible.
*/
@Hidden
- @Argument(fullName="includeUmappedReads", shortName="unmapped", doc="If provided, unmapped reads with chromosomal coordinates (i.e., those placed to their maps) will be included in the assembly and calling", required = false)
+ @Argument(fullName="includeUmappedReads", shortName="unmapped", doc="Include unmapped reads with chromosomal coordinates", required = false)
protected boolean includeUnmappedReads = false;
@Advanced
- @Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "If specified, use additional trigger on variants found in an external alleles file", required=false)
+ @Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "Use additional trigger on variants found in an external alleles file", required=false)
protected boolean USE_ALLELES_TRIGGER = false;
/**
@@ -501,29 +516,33 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
* read for all of these events. With this parameter set to Q30, though, the maximum evidence against any haplotype
* that this (and any) read could contribute is Q30.
*
- * Set this term to any negative number to turn off the global mapping rate
+ * Set this term to any negative number to turn off the global mapping rate.
*/
@Advanced
@Argument(fullName="phredScaledGlobalReadMismappingRate", shortName="globalMAPQ", doc="The global assumed mismapping rate for reads", required = false)
protected int phredScaledGlobalReadMismappingRate = 45;
/**
- * Assembly graph can be quite complex, and could imply a very large number of possible haplotypes. Each haplotype
+ * The assembly graph can be quite complex, and could imply a very large number of possible haplotypes. Each haplotype
* considered requires N PairHMM evaluations if there are N reads across all samples. In order to control the
* run of the haplotype caller we only take maxNumHaplotypesInPopulation paths from the graph, in order of their
* weights, no matter how many paths are possible to generate from the graph. Putting this number too low
* will result in dropping true variation because paths that include the real variant are not even considered.
+ * You can consider increasing this number when calling organisms with high heterozygosity.
*/
@Advanced
- @Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population. This number will probably need to be increased when calling organisms with high heterozygosity.", required = false)
+ @Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population", required = false)
protected int maxNumHaplotypesInPopulation = 128;
@Advanced
- @Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="If specified, we will merge variants together into block substitutions that are in strong local LD", required = false)
+ @Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="Merge variants together into block substitutions if they are in strong local LD", required = false)
protected boolean mergeVariantsViaLD = false;
+ /**
+ * As of GATK 3.3, HaplotypeCaller outputs physical information (see release notes and documentation for details). This argument disables that behavior.
+ */
@Advanced
- @Argument(fullName="doNotRunPhysicalPhasing", shortName="doNotRunPhysicalPhasing", doc="If specified, we will not try to add physical (read-based) phasing information", required = false)
+ @Argument(fullName="doNotRunPhysicalPhasing", shortName="doNotRunPhysicalPhasing", doc="Don't try to add physical (read-based) phasing information", required = false)
protected boolean doNotRunPhysicalPhasing = false;
public static final String HAPLOTYPE_CALLER_PHASING_ID_KEY = "PID";
@@ -543,45 +562,60 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
@Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)
protected String keepRG = null;
+ /**
+ * This argument is intended for benchmarking and scalability testing.
+ */
@Hidden
- @Argument(fullName="justDetermineActiveRegions", shortName="justDetermineActiveRegions", doc = "If specified, the HC won't actually do any assembly or calling, it'll just run the upfront active region determination code. Useful for benchmarking and scalability testing", required=false)
+ @Argument(fullName="justDetermineActiveRegions", shortName="justDetermineActiveRegions", doc = "Just determine ActiveRegions, don't perform assembly or calling", required=false)
protected boolean justDetermineActiveRegions = false;
+ /**
+ * This argument is intended for benchmarking and scalability testing.
+ */
@Hidden
- @Argument(fullName="dontGenotype", shortName="dontGenotype", doc = "If specified, the HC will do any assembly but won't do calling. Useful for benchmarking and scalability testing", required=false)
+ @Argument(fullName="dontGenotype", shortName="dontGenotype", doc = "Perform assembly but do not genotype variants", required=false)
protected boolean dontGenotype = false;
+ /**
+ * Enabling this argument may cause fundamental problems with the assembly graph itself.
+ */
@Hidden
- @Argument(fullName="errorCorrectKmers", shortName="errorCorrectKmers", doc = "Use an exploratory algorithm to error correct the kmers used during assembly. May cause fundamental problems with the assembly graph itself", required=false)
+ @Argument(fullName="errorCorrectKmers", shortName="errorCorrectKmers", doc = "Use an exploratory algorithm to error correct the kmers used during assembly", required=false)
protected boolean errorCorrectKmers = false;
@Hidden
- @Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="If specified, we will write DOT formatted graph files out of the assembler for only this graph size", required = false)
+ @Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="Write DOT formatted graph files out of the assembler for only this graph size", required = false)
protected boolean debugGraphTransformations = false;
@Advanced
- @Argument(fullName="dontUseSoftClippedBases", shortName="dontUseSoftClippedBases", doc="If specified, we will not analyze soft clipped bases in the reads", required = false)
+ @Argument(fullName="dontUseSoftClippedBases", shortName="dontUseSoftClippedBases", doc="Do not analyze soft clipped bases in the reads", required = false)
protected boolean dontUseSoftClippedBases = false;
@Hidden
- @Argument(fullName="captureAssemblyFailureBAM", shortName="captureAssemblyFailureBAM", doc="If specified, we will write a BAM called assemblyFailure.bam capturing all of the reads that were in the active region when the assembler failed for any reason", required = false)
+ @Argument(fullName="captureAssemblyFailureBAM", shortName="captureAssemblyFailureBAM", doc="Write a BAM called assemblyFailure.bam capturing all of the reads that were in the active region when the assembler failed for any reason", required = false)
protected boolean captureAssemblyFailureBAM = false;
@Hidden
- @Argument(fullName="allowCyclesInKmerGraphToGeneratePaths", shortName="allowCyclesInKmerGraphToGeneratePaths", doc="If specified, we will allow cycles in the kmer graphs to generate paths with multiple copies of the path sequenece rather than just the shortest paths", required = false)
+ @Argument(fullName="allowCyclesInKmerGraphToGeneratePaths", shortName="allowCyclesInKmerGraphToGeneratePaths", doc="Allow cycles in the kmer graphs to generate paths with multiple copies of the path sequenece rather than just the shortest paths", required = false)
protected boolean allowCyclesInKmerGraphToGeneratePaths = false;
@Hidden
- @Argument(fullName="noFpga", shortName="noFpga", doc="If provided, disables the use of the FPGA HMM implementation", required = false)
+ @Argument(fullName="noFpga", shortName="noFpga", doc="Disable the use of the FPGA HMM implementation", required = false)
protected boolean noFpga = false;
// Parameters to control read error correction
+ /**
+ * Enabling this argument may cause fundamental problems with the assembly graph itself.
+ */
@Hidden
- @Argument(fullName="errorCorrectReads", shortName="errorCorrectReads", doc = "Use an exploratory algorithm to error correct the kmers used during assembly. May cause fundamental problems with the assembly graph itself", required=false)
+ @Argument(fullName="errorCorrectReads", shortName="errorCorrectReads", doc = "Use an exploratory algorithm to error correct the kmers used during assembly", required=false)
protected boolean errorCorrectReads = false;
+ /**
+ * Enabling this argument may cause fundamental problems with the assembly graph itself.
+ */
@Hidden
- @Argument(fullName="kmerLengthForReadErrorCorrection", shortName="kmerLengthForReadErrorCorrection", doc = "Use an exploratory algorithm to error correct the kmers used during assembly. May cause fundamental problems with the assembly graph itself", required=false)
+ @Argument(fullName="kmerLengthForReadErrorCorrection", shortName="kmerLengthForReadErrorCorrection", doc = "Use an exploratory algorithm to error correct the kmers used during assembly", required=false)
protected int kmerLengthForReadErrorCorrection = 25;
@Hidden
@@ -730,7 +764,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
SCAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(SCAC.CONTAMINATION_FRACTION_FILE, SCAC.CONTAMINATION_FRACTION, sampleSet, logger));
if( SCAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES && consensusMode )
- throw new UserException("HaplotypeCaller cannot be run in both GENOTYPE_GIVEN_ALLELES mode and in consensus mode. Please choose one or the other.");
+ throw new UserException("HaplotypeCaller cannot be run in both GENOTYPE_GIVEN_ALLELES mode and in consensus mode at the same time. Please choose one or the other.");
final GenomeLocParser genomeLocParser = toolkit.getGenomeLocParser();
@@ -828,7 +862,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
referenceConfidenceModel = new ReferenceConfidenceModel(getToolkit().getGenomeLocParser(), samples, getToolkit().getSAMFileHeader(), indelSizeToEliminateInRefModel);
if ( emitReferenceConfidence() ) {
if ( samples.sampleCount() != 1 )
- throw new UserException.BadArgumentValue("emitRefConfidence", "Can only be used in single sample mode currently. Use the sample_name argument");
+ throw new UserException.BadArgumentValue("emitRefConfidence", "Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file.");
headerInfo.addAll(referenceConfidenceModel.getVCFHeaderLines());
if ( SCAC.emitReferenceConfidence == ReferenceConfidenceMode.GVCF ) {
// a kluge to enforce the use of this indexing strategy
@@ -862,7 +896,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
default:
//Note: we do not include in the error message list as it is of no grand public interest.
throw new UserException("Unsupported likelihood calculation engine '" + likelihoodCalculationEngine +
- "'. Please use one of the following instead: 'PairHMM' and 'GraphBased'.");
+ "'. Please use one of the following instead: 'PairHMM' or 'GraphBased'.");
}
}
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
index d2881f131..c5d0073f2 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
@@ -63,11 +63,11 @@ import org.broadinstitute.gatk.utils.commandline.Argument;
public class HaplotypeCallerArgumentCollection extends StandardCallerArgumentCollection {
@Advanced
- @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information about each triggering active region", required = false)
+ @Argument(fullName="debug", shortName="debug", doc="Print out very verbose debug information about each triggering active region", required = false)
protected boolean DEBUG;
@Advanced
- @Argument(fullName="useFilteredReadsForAnnotations", shortName="useFilteredReadsForAnnotations", doc = "If specified, use the contamination-filtered read maps for the purposes of annotating variants", required=false)
+ @Argument(fullName="useFilteredReadsForAnnotations", shortName="useFilteredReadsForAnnotations", doc = "Use the contamination-filtered read maps for the purposes of annotating variants", required=false)
protected boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;
/**
@@ -77,7 +77,7 @@ public class HaplotypeCallerArgumentCollection extends StandardCallerArgumentCol
* This requirement is a temporary workaround for an issue with index compression.
*/
@Advanced
- @Argument(fullName="emitRefConfidence", shortName="ERC", doc="Mode for emitting experimental reference confidence scores", required = false)
+ @Argument(fullName="emitRefConfidence", shortName="ERC", doc="Mode for emitting reference confidence scores", required = false)
protected ReferenceConfidenceMode emitReferenceConfidence = ReferenceConfidenceMode.NONE;
@Override
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
index cfe22879b..db9d082b7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
@@ -147,7 +147,7 @@ import java.util.*;
* -R ref.fasta \
* -T SelectVariants \
* --variant input.vcf \
- * -bed family.ped \
+ * -ped family.ped \
* -mvq 50 \
* -o violations.vcf
*