diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 12c893da8..165828013 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -847,7 +847,8 @@ public class GenomeAnalysisEngine { generateExtendedEvents(), getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_INPUT ? argCollection.BAQMode : BAQ.CalculationMode.OFF, getWalkerBAQQualityMode(), - refReader); + refReader, + argCollection.defaultBaseQualities); } /** diff --git a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java index 87c8939c7..14b17f265 100755 --- a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java +++ b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java @@ -41,6 +41,7 @@ public class ReadProperties { private BAQ.CalculationMode cmode = BAQ.CalculationMode.OFF; private BAQ.QualityMode qmode = BAQ.QualityMode.DONT_MODIFY; IndexedFastaSequenceFile refReader = null; // read for BAQ, if desired + private byte defaultBaseQualities; // do we want to generate additional piles of "extended" events (indels) // immediately after the reference base such event is associated with? @@ -135,6 +136,13 @@ public class ReadProperties { return refReader; } + /** + * @return Default base quality value to fill reads missing base quality information. + */ + public byte defaultBaseQualities() { + return defaultBaseQualities; + } + /** * Extract the command-line arguments having to do with reads input * files and store them in an easy-to-work-with package. Constructor @@ -156,6 +164,7 @@ public class ReadProperties { * @param cmode How should we apply the BAQ calculation to the reads? * @param qmode How should we apply the BAQ calculation to the reads? * @param refReader if applyBAQ is true, must be a valid pointer to a indexed fasta file reads so we can get the ref bases for BAQ calculation + * @param defaultBaseQualities if the reads have incomplete quality scores, set them all to defaultBaseQuality. */ public ReadProperties( Collection samFiles, SAMFileHeader header, @@ -169,7 +178,8 @@ public class ReadProperties { boolean generateExtendedEvents, BAQ.CalculationMode cmode, BAQ.QualityMode qmode, - IndexedFastaSequenceFile refReader ) { + IndexedFastaSequenceFile refReader, + byte defaultBaseQualities) { this.readers = samFiles; this.header = header; this.readBufferSize = readBufferSize; @@ -183,5 +193,6 @@ public class ReadProperties { this.cmode = cmode; this.qmode = qmode; this.refReader = refReader; + this.defaultBaseQualities = defaultBaseQualities; } } diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 1f758b0f6..7d4716276 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -185,6 +185,9 @@ public class GATKArgumentCollection { @Argument(fullName="useOriginalQualities", shortName = "OQ", doc = "If set, use the original base quality scores from the OQ tag when present instead of the standard scores", required=false) public Boolean useOriginalBaseQualities = false; + @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false) + public byte defaultBaseQualities = -1; + @Element(required = false) @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false) public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java index aef2b0bcc..09dc64bca 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java @@ -140,8 +140,7 @@ public class SAMDataSource implements SimpleDataSource { new ValidationExclusion(), new ArrayList(), false, - false - ); + false); } /** @@ -157,7 +156,7 @@ public class SAMDataSource implements SimpleDataSource { ValidationExclusion exclusionList, Collection supplementalFilters, boolean includeReadsWithDeletionAtLoci, - boolean generateExtendedEvents ) { + boolean generateExtendedEvents) { this( samFiles, genomeLocParser, useOriginalBaseQualities, @@ -168,7 +167,10 @@ public class SAMDataSource implements SimpleDataSource { supplementalFilters, includeReadsWithDeletionAtLoci, generateExtendedEvents, - BAQ.CalculationMode.OFF, BAQ.QualityMode.DONT_MODIFY, null // no BAQ + BAQ.CalculationMode.OFF, + BAQ.QualityMode.DONT_MODIFY, + null, // no BAQ + (byte) -1 ); } @@ -187,6 +189,7 @@ public class SAMDataSource implements SimpleDataSource { * @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method * will explicitly list reads with deletion over the current reference base; otherwise, only observed * bases will be seen in the pileups, and the deletions will be skipped silently. + * @param defaultBaseQualities if the reads have incomplete quality scores, set them all to defaultBaseQuality. */ public SAMDataSource( Collection samFiles, @@ -201,8 +204,8 @@ public class SAMDataSource implements SimpleDataSource { boolean generateExtendedEvents, BAQ.CalculationMode cmode, BAQ.QualityMode qmode, - IndexedFastaSequenceFile refReader - ) { + IndexedFastaSequenceFile refReader, + byte defaultBaseQualities) { this.readMetrics = new ReadMetrics(); this.genomeLocParser = genomeLocParser; @@ -248,7 +251,10 @@ public class SAMDataSource implements SimpleDataSource { supplementalFilters, includeReadsWithDeletionAtLoci, generateExtendedEvents, - cmode, qmode, refReader ); + cmode, + qmode, + refReader, + defaultBaseQualities); // cache the read group id (original) -> read group id (merged) // and read group id (merged) -> read group id (original) mappings. @@ -521,7 +527,10 @@ public class SAMDataSource implements SimpleDataSource { readProperties.getDownsamplingMethod().toFraction, readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION), readProperties.getSupplementalFilters(), - readProperties.getBAQCalculationMode(), readProperties.getBAQQualityMode(), readProperties.getRefReader()); + readProperties.getBAQCalculationMode(), + readProperties.getBAQQualityMode(), + readProperties.getRefReader(), + readProperties.defaultBaseQualities()); } /** @@ -545,7 +554,10 @@ public class SAMDataSource implements SimpleDataSource { readProperties.getDownsamplingMethod().toFraction, readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION), readProperties.getSupplementalFilters(), - readProperties.getBAQCalculationMode(), readProperties.getBAQQualityMode(), readProperties.getRefReader()); + readProperties.getBAQCalculationMode(), + readProperties.getBAQQualityMode(), + readProperties.getRefReader(), + readProperties.defaultBaseQualities()); } /** @@ -570,6 +582,7 @@ public class SAMDataSource implements SimpleDataSource { * @param downsamplingFraction whether and how much to downsample the reads themselves (not at a locus). * @param noValidationOfReadOrder Another trigger for the verifying iterator? TODO: look into this. * @param supplementalFilters additional filters to apply to the reads. + * @param defaultBaseQualities if the reads have incomplete quality scores, set them all to defaultBaseQuality. * @return An iterator wrapped with filters reflecting the passed-in parameters. Will not be null. */ protected StingSAMIterator applyDecoratingIterators(ReadMetrics readMetrics, @@ -579,8 +592,11 @@ public class SAMDataSource implements SimpleDataSource { Double downsamplingFraction, Boolean noValidationOfReadOrder, Collection supplementalFilters, - BAQ.CalculationMode cmode, BAQ.QualityMode qmode, IndexedFastaSequenceFile refReader ) { - wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities); + BAQ.CalculationMode cmode, + BAQ.QualityMode qmode, + IndexedFastaSequenceFile refReader, + byte defaultBaseQualities) { + wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities, defaultBaseQualities); // NOTE: this (and other filtering) should be done before on-the-fly sorting // as there is no reason to sort something that we will end of throwing away diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java index bbe95096e..239392eec 100644 --- a/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java @@ -32,14 +32,23 @@ public class ReadFormattingIterator implements StingSAMIterator { */ private final boolean useOriginalBaseQualities; + /** + * Positive if there is a default Base Quality value to fill in the reads with. + */ + private final byte defaultBaseQualities; + + /** * Decorate the given iterator inside a ReadWrappingIterator. * @param wrappedIterator iterator * @param useOriginalBaseQualities true if original base qualities should be used + * @param defaultBaseQualities if the reads have incomplete quality scores, set them all to defaultBaseQuality. */ - public ReadFormattingIterator(StingSAMIterator wrappedIterator, boolean useOriginalBaseQualities) { + public ReadFormattingIterator(StingSAMIterator wrappedIterator, boolean useOriginalBaseQualities, byte defaultBaseQualities) { this.wrappedIterator = wrappedIterator; this.useOriginalBaseQualities = useOriginalBaseQualities; + this.defaultBaseQualities = defaultBaseQualities; + } /** @@ -74,7 +83,7 @@ public class ReadFormattingIterator implements StingSAMIterator { * no next exists. */ public SAMRecord next() { - return new GATKSAMRecord(wrappedIterator.next(), useOriginalBaseQualities); + return new GATKSAMRecord(wrappedIterator.next(), useOriginalBaseQualities, defaultBaseQualities); } /** diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index dc56c3775..3536e847d 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -50,7 +50,7 @@ public class GATKSAMRecord extends SAMRecord { // TODO: this is a temporary hack. If it works, clean it up. private BitSet mBitSet = null; - public GATKSAMRecord(SAMRecord record, boolean useOriginalBaseQualities) { + public GATKSAMRecord(SAMRecord record, boolean useOriginalBaseQualities, byte defaultBaseQualities) { super(null); // it doesn't matter - this isn't used if ( record == null ) throw new IllegalArgumentException("The SAMRecord argument cannot be null"); @@ -65,6 +65,20 @@ public class GATKSAMRecord extends SAMRecord { for ( SAMTagAndValue attribute : attributes ) setAttribute(attribute.tag, attribute.value); + // if we are using default quals, check if we need them, and add if necessary. + // 1. we need if reads are lacking or have incomplete quality scores + // 2. we add if defaultBaseQualities has a positive value + if (defaultBaseQualities >= 0) { + byte reads [] = record.getReadBases(); + byte quals [] = record.getBaseQualities(); + if (quals == null || quals.length < reads.length) { + byte new_quals [] = new byte [reads.length]; + for (int i=0; i(), false, false, - BAQ.CalculationMode.OFF, BAQ.QualityMode.DONT_MODIFY, null // no BAQ + BAQ.CalculationMode.OFF, + BAQ.QualityMode.DONT_MODIFY, + null, // no BAQ + (byte) -1 ); } } diff --git a/scala/qscript/carneiro/tdPipeline.scala b/scala/qscript/carneiro/tdPipeline.scala new file mode 100755 index 000000000..b90b10774 --- /dev/null +++ b/scala/qscript/carneiro/tdPipeline.scala @@ -0,0 +1,214 @@ +import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.sting.queue.QScript +//import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction +//import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction +//import org.apache.commons.io.FilenameUtils; + +class tdPipeline extends QScript { + qscript => + + @Argument(shortName="gatk", doc="gatk jar file", required=true) + var gatkJarFile: File = _ + + @Argument(shortName="outputDir", doc="output directory", required=true) + var outputDir: String = "./" + + @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false) + var useBAQ: Boolean = true + + @Argument(shortName="noMask", doc="turns off MASK calculation", required=false) + var useMask: Boolean = true + + + trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(4);} + + class Target( + val baseName: String, + val reference: File, + val dbsnpFile: String, + val hapmapFile: String, + val maskFile: String, + val bamList: File, + val goldStandard_VCF: File, + val intervals: String, + val titvTarget: Double, + val isLowpass: Boolean) { + val name = qscript.outputDir + baseName + val clusterFile = new File(name + ".clusters") + val rawVCF = new File(name + ".raw.vcf") + val filteredVCF = new File(name + ".filtered.vcf") + val goldStandardName = qscript.outputDir + "goldStandard/" + baseName + val goldStandardClusterFile = new File(goldStandardName + ".clusters") + } + + val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") + val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta") + val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta") + + // Define the target datasets here + val lowPass: Boolean = true + val HiSeq = new Target("NA12878.HiSeq", + hg18, + "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_hg18.rod", + "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.hg18_fwd.vcf", + "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.bed", + new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"), + new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", + 2.07, + !lowPass) + + val LowPassFIN79Nov = new Target("FIN.nov2010", + b37, + "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf", + "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf", + "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.hg18.bed", + new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"), + new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", + 2.3, + lowPass) + + /* + * These sources need to be updated, never used. + + val TGPWExGdA = new Target("1000G.WEx.GdA", b37, "b37", + new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people + new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** + "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass) + val WEx = new Target("NA12878.WEx", hg18, "hg18", + new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"), + new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"), + "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, !lowPass) + val LowPassN60 = new Target("lowpass.N60", b36, "b36", // which reference the data is aligned to + new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from + new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), // the gold standard VCF file to run through the VQSR + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, lowPass) // chunked interval list to use with Queue's scatter/gather functionality + val LowPassAugust = new Target("ALL.august.v4", b37, "b37", // BUGBUG: kill this, it is too large + new File("/humgen/1kg/processing/allPopulations_chr20_august_release.cleaned.merged.bams/ALL.cleaned.merged.list"), + new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass) + val LowPassEUR363Nov = new Target("EUR.nov2010", b37, "b37", + new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"), + new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass) + */ + val targets = List(HiSeq, LowPassFIN79Nov) + + def script = { + val goldStandard = true + for (target <- targets) { + add(new UnifiedGenotyper(target)) + add(new VariantFiltration(target)) + add(new GenerateVariantClusters(target, !goldStandard)) + add(new VariantRecalibratorTiTv(target, !goldStandard)) + add(new VariantRecalibratorNRS(target, !goldStandard)) + add(new VariantEvaluation(target)) + } + } + + val FiltersToIgnore = List("DPFilter", "ABFilter", "ESPStandard", "QualByDepth", "StrandBias", "HomopolymerRun") + + // 1.) Call SNPs with UG + class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS { + this.reference_sequence = t.reference + if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile) + else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) + this.intervalsString ++= List(t.intervals) + this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20 + this.jobQueue = "hour" + this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } ) + this.input_file :+= t.bamList + this.out = t.rawVCF + if (useBAQ) + this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE) + else + this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF) + this.stand_call_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) + this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) + this.analysisName = t.name + "_UG" + } + + // 2.) Filter SNPs + class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration with UNIVERSAL_GATK_ARGS { + this.reference_sequence = t.reference + this.intervalsString ++= List(t.intervals) + this.scatterCount = 10 + this.jobQueue = "hour" + this.variantVCF = t.rawVCF + this.out = t.filteredVCF + if (useMask) { + this.rodBind :+= RodBind("mask", "Bed", t.maskFile) + this.maskName = "InDel" + } + this.filterName ++= List("HARD_TO_VALIDATE") + this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"") + this.analysisName = t.name + "_VF" + } + + // 3.) VQSR part1 Generate Gaussian clusters based on truth sites + class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS { + val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name } + this.reference_sequence = t.reference + if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile) + else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) + this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile) + this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } ) + this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile } + this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") + this.analysisName = name + "_GVC" + this.intervalsString ++= List(t.intervals) + this.qual = Some(300) // clustering parameters to be updated soon pending new experimentation results + this.std = Some(3.5) + this.mG = Some(16) + this.ignoreFilter ++= FiltersToIgnore + } + + // 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters + class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS { + val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name } + this.reference_sequence = t.reference + if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile) + else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) + this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile) + this.rodBind :+= RodBind("truth", "VCF", t.hapmapFile) + this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } ) + this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile } + this.analysisName = name + "_VR" + this.intervalsString ++= List(t.intervals) + this.ignoreFilter ++= FiltersToIgnore + this.ignoreFilter ++= List("HARD_TO_VALIDATE") + this.priorDBSNP = Some(2.0) + this.priorHapMap = Some(2.0) + this.target_titv = t.titvTarget + } + + // 4a.) Choose VQSR tranches based on novel ti/tv + class VariantRecalibratorTiTv(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) { + this.tranche ++= List("0.1", "1.0", "10.0", "100.0") + this.out = new File(this.name + ".titv.recalibrated.vcf") + this.tranchesFile = new File(this.name + ".titv.tranches") + } + + // 4b.) Choose VQSR tranches based on sensitivity to truth set + class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) { + this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) + this.tranche ++= List("0.1", "1.0", "10.0", "100.0") + this.out = new File(this.name + ".ts.recalibrated.vcf") + this.tranchesFile = new File(this.name + ".ts.tranches") + } + + // 5.) Variant Evaluation generates the csv files for Genome Concordance analysis + class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS { + val name: String = t.name + this.reference_sequence = t.reference + if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile) + else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) + this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile) + this.rodBind :+= RodBind("input", "VCF", t.filteredVCF) + this.analysisName = name + "_VR" + this.intervalsString ++= List(t.intervals) + this.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R) + this.reportLocation = new File(t.name + ".eval") + } +}