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Change key Haplotype default parameter values 

-- Extension increased to 200 bp
-- Min prune factor defaults to 0
-- LD merging enabled by default for complex variants, only when there are 10+ samples for SNP + SNP merging
-- Active region trimming enabled by default
This commit is contained in:
Mark DePristo 2013-04-04 20:29:17 -04:00
parent 3a19266843
commit 5a54a4155a
1 changed files with 11 additions and 12 deletions
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23
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -137,7 +137,7 @@ import java.util.*;
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionTraversalParameters(extension=85, maxRegion=300)
@ActiveRegionTraversalParameters(extension=200, maxRegion=300)
@ReadFilters({HCMappingQualityFilter.class})
@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
@ -200,7 +200,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@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)
protected int MIN_PRUNE_FACTOR = 1;
protected int MIN_PRUNE_FACTOR = 0;
@Advanced
@Argument(fullName="gcpHMM", shortName="gcpHMM", doc="Flat gap continuation penalty for use in the Pair HMM", required = false)
@ -284,6 +284,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
protected List<String> annotationsToExclude = new ArrayList<String>(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator"}));
@Advanced
@Argument(fullName="dontMergeVariantsViaLD", shortName="dontMergeVariantsViaLD", doc="If specified, we will include low quality bases when doing the assembly", required = false)
protected boolean dontMergeVariantsViaLD = false;
/**
* Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
*/
@ -301,18 +305,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@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)
protected int debugGraphTransformations = -1;
// TODO -- not currently useful
@Hidden
@Hidden // TODO -- not currently useful
@Argument(fullName="useLowQualityBasesForAssembly", shortName="useLowQualityBasesForAssembly", doc="If specified, we will include low quality bases when doing the assembly", required = false)
protected boolean useLowQualityBasesForAssembly = false;
@Hidden
@Argument(fullName="useNewLDMerger", shortName="useNewLDMerger", doc="If specified, we will include low quality bases when doing the assembly", required = false)
protected boolean useNewLDMerger = false;
@Hidden
@Argument(fullName="trimActiveRegions", shortName="trimActiveRegions", doc="If specified, we will trim down the active region from the full region (active + extension) to just the active interval for genotyping", required = false)
protected boolean trimActiveRegions = false;
@Argument(fullName="dontTrimActiveRegions", shortName="donTrimActiveRegions", doc="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping", required = false)
protected boolean dontTrimActiveRegions = 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)
@ -437,7 +436,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
final LDMerger ldMerger = new LDMerger(DEBUG, useNewLDMerger ? 10 : 10, useNewLDMerger ? 1 : 10);
final LDMerger ldMerger = new LDMerger(DEBUG, dontMergeVariantsViaLD ? 10000000 : 10, dontMergeVariantsViaLD ? 10000000 : 1);
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS, ldMerger );
@ -640,7 +639,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
final List<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, activeAllelesToGenotype );
if ( trimActiveRegions ) {
if ( ! dontTrimActiveRegions ) {
return trimActiveRegion(activeRegion, haplotypes, fullReferenceWithPadding, paddedReferenceLoc);
} else {
// we don't want to or cannot create a trimmed active region, so go ahead and use the old one