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-baqGOP now takes phred scaled scores instead of probabilities in the command line. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4982 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-01-13 00:06:38 +00:00
parent 5736d2e2bb
commit 9e93091e9a
3 changed files with 67 additions and 27 deletions
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2
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -162,7 +162,7 @@ public class GATKArgumentCollection {
public BAQ.CalculationMode BAQMode = BAQ.CalculationMode.OFF;
@Element(required = false)
@Argument(fullName = "baqGapOpenPenalty", shortName="baqGOP", doc="BAQ gap open penalty. Default value is 1e-4. 1e-3 is perhaps better for whole genome call sets", required = false)
@Argument(fullName = "baqGapOpenPenalty", shortName="baqGOP", doc="BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets", required = false)
public double BAQGOP = BAQ.DEFAULT_GOP;
// --------------------------------------------------------------------------------------------------------------

19
java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -64,7 +64,18 @@ public class BAQ {
qual2prob[i] = Math.pow(10, -i/10.);
}
public static double DEFAULT_GOP = 1e-4;
// Phred scaled now (changed 1/10/2011)
public static double DEFAULT_GOP = 40;
/* Takes a Phred Scale quality score and returns the error probability.
*
* Quick conversion function to maintain internal structure of BAQ calculation on
* probability scale, but take the user entered parameter in phred-scale.
*
* @param x phred scaled score
* @return probability of incorrect base call
*/
private double convertFromPhredScale(double x) { return (Math.pow(10,(-x)/10.));}
public double cd = -1; // gap open probility [1e-3]
private double ce = 0.1; // gap extension probability [0.1]
@ -96,14 +107,14 @@ public class BAQ {
* Use defaults for everything
*/
public BAQ() {
cd = DEFAULT_GOP;
cd = convertFromPhredScale(DEFAULT_GOP);
initializeCachedData();
}
/**
* Create a new HmmGlocal object with specified parameters
*
* @param d gap open prob.
* @param d gap open prob (not phred scaled!).
* @param e gap extension prob.
* @param b band width
* @param minBaseQual All bases with Q < minBaseQual are up'd to this value
@ -591,4 +602,4 @@ public class BAQ {
// keeping mapped reads, regardless of pairing status, or primary alignment status.
return read.getReadUnmappedFlag() || read.getReadFailsVendorQualityCheckFlag() || read.getDuplicateReadFlag();
}
}
}

73
scala/qscript/carneiro/tdPipeline.scala
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@ -14,10 +14,10 @@ class tdPipeline extends QScript {
var outputDir: String = "./"
@Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
var useBAQ: Boolean = true
var noBAQ: Boolean = false
@Argument(shortName="noMask", doc="turns off MASK calculation", required=false)
var useMask: Boolean = true
var noMask: Boolean = false
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(4);}
@ -37,6 +37,8 @@ class tdPipeline extends QScript {
val clusterFile = new File(name + ".clusters")
val rawVCF = new File(name + ".raw.vcf")
val filteredVCF = new File(name + ".filtered.vcf")
val titvRecalibratedVCF = new File(name + ".titv.recalibrated.vcf")
val tsRecalibratedVCF = new File(name + ".ts.recalibrated.vcf")
val goldStandardName = qscript.outputDir + "goldStandard/" + baseName
val goldStandardClusterFile = new File(goldStandardName + ".clusters")
}
@ -51,35 +53,64 @@ class tdPipeline extends QScript {
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",
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
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",
val FIN = new Target("FIN",
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",
"/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b37.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)
val WEx = new Target("NA12878.WEx",
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/GA2.WEx.cleaned.indels.10.mask",
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 WEx1kg = new Target("1000G.WEx.GdA",
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.b37.bed",
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)
/*
// Needs an interval file, and a decent TiTv estimate.
val PacBio = new Target("pacbio",
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.b37.bed",
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/pb_reads.18.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/pb_reads.18.recal.bam"),
"",
2.00,
!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
@ -93,7 +124,8 @@ class tdPipeline extends QScript {
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)
val targets = List(HiSeq)
def script = {
val goldStandard = true
@ -116,14 +148,10 @@ class tdPipeline extends QScript {
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.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE})
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"
@ -134,10 +162,9 @@ class tdPipeline extends QScript {
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) {
if (!noMask) {
this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
this.maskName = "InDel"
}
@ -205,10 +232,12 @@ class tdPipeline extends QScript {
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.rodBind :+= RodBind("eval", "VCF", t.tsRecalibratedVCF)
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")
this.noStandard = true
this.evalModule ++= List("TiTvVariantEvaluator", "CountVariants", "GenotypeConcordance")
}
}