507 lines
24 KiB
Plaintext
Executable File
507 lines
24 KiB
Plaintext
Executable File
import java.io.{FileReader, File, BufferedReader}
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import net.sf.picard.reference.FastaSequenceFile
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import org.broadinstitute.sting.datasources.pipeline.Pipeline
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
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import org.broadinstitute.sting.gatk.DownsampleType
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import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.samtools._
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import org.broadinstitute.sting.queue.{QException, QScript}
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import collection.JavaConversions._
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import org.broadinstitute.sting.utils.yaml.YamlUtils
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import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
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import scala.collection.mutable.HashMap
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class omni_qc extends QScript {
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qscript =>
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// NON-OMNI VCF FILES
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var pilot3_release_vcf = new TaggedFile("/humgen/gsa-scr1/chartl/projects/pilot3/merge_release/ALL.exon.2010_03.genotypes.vcf","vcf")
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var pilot1_ceu_vcf = new TaggedFile("/humgen/1kg/releases/pilot_project/2010_07/low_coverage/snps/CEU.low_coverage.2010_07.genotypes.vcf.gz","vcf")
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var pilot1_chb_vcf = new TaggedFile("/humgen/1kg/releases/pilot_project/2010_07/low_coverage/snps/CHBJPT.low_coverage.2010_07.genotypes.vcf.gz","vcf")
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var pilot1_yri_vcf = new TaggedFile("/humgen/1kg/releases/pilot_project/2010_07/low_coverage/snps/YRI.low_coverage.2010_07.genotypes.vcf.gz","vcf")
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var august_calls_EUR = new TaggedFile("/humgen/1kg/processing/release/august/EUR.vcf","vcf")
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var august_calls_ASN = new TaggedFile("/humgen/1kg/processing/release/august/ASN.vcf","vcf")
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var august_calls_AFR = new TaggedFile("/humgen/1kg/processing/release/august/AFR.vcf","vcf")
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var august_calls_EUR_refined = new TaggedFile("/humgen/1kg/processing/release/august/bgzip_for_release/EUR.beagle.vcf.gz","vcf")
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var august_calls_ASN_refined = new TaggedFile("/humgen/1kg/processing/release/august/bgzip_for_release/ASN.beagle.vcf.gz","vcf")
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var august_calls_AFR_refined = new TaggedFile("/humgen/1kg/processing/release/august/bgzip_for_release/AFR.beagle.vcf.gz","vcf")
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var hiseq_calls_vcf = new TaggedFile("/humgen/gsa-scr1/chartl/projects/omni/resources/NA12878.HiSeq.v9.b36.vcf.gz","vcf")
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var pilot1_with_na12878_vcf = new TaggedFile("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/calls/v2/N60/lowpass.N60.recal.mG6.retranche.vcf","vcf")
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var pilot1_na12878_beagle = new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/calls/beagle/lowpass.N60.recal.CEUTSI.bgl.output.vcf")
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//var august_calls_other_genotypes = _
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// OMNI VCF FILES
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var OMNI_b36_vcf = new TaggedFile("/humgen/illumina/1kg_seq_vcfs/Illumina_HapMap_Omni_2.5_764samples.vcf","vcf")
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var OMNI_b37_vcf = new TaggedFile("/broad/shptmp/chartl/Omni_2.5_764_samples.b37.deduped.vcf","vcf")
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var OMNI_hapmap_b36_vcf = new TaggedFile("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/Omni_2_5_pilot.b36.vcf","vcf")
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var OMNI_b36_panel_vcf = new TaggedFile("/broad/shptmp/chartl/omni/vcfs/Omni_b36_with_panel_sets.vcf","vcf")
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var OMNI_b37_birdseed = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/OMNI_birdseed_only.vcf")
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var OMNI_b37_joint = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/OMNI_joint_birdseed_lowpass.vcf")
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// INTERVALS
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var pilot3_interval_list: String = "/humgen/gsa-hpprojects/1kg/1kg_pilot3/documents/CenterSpecificTargetLists/results/p3overlap.targets.b36.interval_list"
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var pilot1_interval_list: String = "/broad/shptmp/chartl/omni/resources/Omni_b36_sites.interval.list"
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var hiseq_interval_list: String = "/broad/shptmp/chartl/omni/resources/Omni_b36_sites.interval.list"
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var production_interval_list: String = "/broad/shptmp/chartl/omni/resources/Omni_b37_sites.chr20.interval.list"
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// REFERENCES
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var b36_ref = new File("/humgen/1kg/reference/human_b36_both.fasta")
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var b37_ref = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
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// OTHER
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val analysis_dir = "/broad/shptmp/chartl/omni/"
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val resources_dir = analysis_dir + "resources/"
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val scratch_dir = analysis_dir + "scratch/"
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val eval_dir = analysis_dir + "eval/"
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val vcf_dir = analysis_dir + "vcfs/"
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val p1_ceu_only = scratch_dir+"Pilot1_CEU_only_sites.intervals.list"
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val p1_chbjpt_only = scratch_dir+"Pilot1_CHBJPT_only_sites.intervals.list"
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val p1_yri_only = scratch_dir+"Pilot1_YRI_only_sites.intervals.list"
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// OTHER CHIPS
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val OMNI_QUAD_1KG = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/other_chips/1KG_OMNI.ref_fixed.vcf")
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val AFFY_6_0 = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/other_chips/1KG_ARRAY.ref_fixed.vcf")
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trait OmniArgs extends CommandLineGATK {
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this.jarFile = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar")
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}
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class vcf2bed extends CommandLineFunction {
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@Input(doc="A VCF file to be put into an interval list") var in_vcf: File = _
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@Output(doc="An interval list file to be used with -L") var out_list: File = _
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def commandLine = "python /humgen/gsa-scr1/chartl/projects/omni/scripts/vcf2bed.py %s %s".format(in_vcf.getAbsolutePath,out_list.getAbsolutePath)
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}
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class GetSampleOverlap extends CommandLineFunction {
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@Input(doc="A list of VCF files for which to calculate the sample overlap") var in_vcfs: List[File] = Nil
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@Output(doc="A file to which to write the overlapping sample names") var outFile: File = _
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/*def commandLine = "grep #CHR %s | sed 's/.vcf:/\\t/g' | cut -f11- | tr '\\t' '\\n' | sort | uniq -c | awk '$1 == %d' | awk '{print $2}' > %s".format(
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in_vcfs.foldLeft[String]("")( (str,f) => if ( str.equals("") ) str + f.getAbsolutePath else str + " " + f.getAbsolutePath),
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in_vcfs.size,
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outFile.getAbsolutePath
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)*/
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def commandLine = "python /humgen/gsa-scr1/chartl/projects/omni/scripts/getOverlapSamples.py %s %s".format(
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in_vcfs.foldLeft[String]("")( (str,f) => if ( str.equals("") ) str + f.getAbsolutePath else str + " " + f.getAbsolutePath),
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outFile.getAbsolutePath
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)
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}
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class GunzipFile extends CommandLineFunction {
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@Input(doc="file to gunzip") var gunzipMe: File = _
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@Output(doc="file to gunzip to") var outFile: File = _
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def commandLine = "gunzip -c %s > %s".format(gunzipMe.getAbsolutePath,outFile.getAbsolutePath)
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}
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def script = {
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/** Convert other chips to merged VCFs **/
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//var august_call_other_chips: List[(String,File)] = processAuxiliaryChipData(august_calls_other_genotypes)
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/** Unzip the pilot 1 VCFs and dump them into the resources directory **/
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var gunzip_p1_ceu = new GunzipFile
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var gunzip_p1_chb = new GunzipFile
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var gunzip_p1_yri = new GunzipFile
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var gunzip_hiseq = new GunzipFile
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var gunzip_ag_eur = new GunzipFile
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var gunzip_ag_asn = new GunzipFile
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var gunzip_ag_afr = new GunzipFile
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gunzip_p1_ceu.gunzipMe = pilot1_ceu_vcf
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gunzip_p1_ceu.outFile = new File(resources_dir+"CEU.low_coverage.genotypes.vcf")
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gunzip_p1_chb.gunzipMe = pilot1_chb_vcf
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gunzip_p1_chb.outFile = new File(resources_dir+"CHB.low_coverage.genotypes.vcf")
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gunzip_p1_yri.gunzipMe = pilot1_yri_vcf
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gunzip_p1_yri.outFile = new File(resources_dir+"YRI.low_coverage.genotypes.vcf")
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gunzip_hiseq.gunzipMe = hiseq_calls_vcf
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gunzip_hiseq.outFile = new File(resources_dir+"HiSeq.b36.vcf")
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gunzip_ag_eur.gunzipMe = august_calls_EUR_refined
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gunzip_ag_eur.outFile = new File(resources_dir+"EUR.refined.vcf")
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gunzip_ag_asn.gunzipMe = august_calls_ASN_refined
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gunzip_ag_asn.outFile = new File(resources_dir+"ASN.refined.vcf")
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gunzip_ag_afr.gunzipMe = august_calls_AFR_refined
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gunzip_ag_afr.outFile = new File(resources_dir+"AFR.refined.vcf")
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add(gunzip_p1_ceu,gunzip_p1_yri,gunzip_p1_chb,gunzip_hiseq,gunzip_ag_eur,gunzip_ag_asn,gunzip_ag_afr)
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/** fix the omni ref bases **/
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var fix_421 = new FixRefBases with OmniArgs
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var fix_764 = new FixRefBases with OmniArgs
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var fix_764_b37 = new FixRefBases with OmniArgs
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fix_421.variantVCF = OMNI_hapmap_b36_vcf
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fix_421.reference_sequence = b36_ref
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fix_421.out = new File(vcf_dir+swapExt(OMNI_hapmap_b36_vcf.getName,".vcf",".ref_fixed.vcf"))
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fix_421.bypassException = true
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fix_764.variantVCF = OMNI_b36_vcf
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fix_764.reference_sequence = b36_ref
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fix_764.out = new File(vcf_dir+swapExt(OMNI_b36_vcf.getName,".vcf",".ref_fixed.vcf"))
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fix_764.bypassException = true
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fix_764_b37.variantVCF = OMNI_b37_vcf
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fix_764_b37.reference_sequence = b37_ref
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fix_764_b37.out = new File(vcf_dir+swapExt(OMNI_b37_vcf.getName,".vcf",".ref_fixed.vcf"))
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fix_764_b37.bypassException = true
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add(fix_421,fix_764,fix_764_b37)
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/** Propagate AC/AN annotations to Omni files via variant annotator **/
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var annotate_421 = new VariantAnnotator with OmniArgs
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var annotate_764 = new VariantAnnotator with OmniArgs
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var annotate_764_b37 = new VariantAnnotator with OmniArgs
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annotate_421.variantVCF = OMNI_hapmap_b36_vcf
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annotate_421.reference_sequence = b36_ref
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annotate_421.annotation :+= "ChromosomeCounts"
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annotate_421.out = new File(vcf_dir+swapExt(annotate_421.variantVCF.getName,".vcf",".annot.vcf"))
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annotate_764.variantVCF = OMNI_b36_vcf
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annotate_764.reference_sequence = b36_ref
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annotate_764.annotation :+= "ChromosomeCounts"
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annotate_764.out = new File(vcf_dir+swapExt(annotate_764.variantVCF.getName,".vcf",".annot.vcf"))
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annotate_764_b37.variantVCF = OMNI_b37_vcf
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annotate_764_b37.reference_sequence = b37_ref
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annotate_764_b37.annotation :+= "ChromosomeCounts"
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annotate_764_b37.out = new File(vcf_dir+swapExt(annotate_764_b37.variantVCF.getName,".vcf",".annot.vcf"))
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add(annotate_421,annotate_764,annotate_764_b37)
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/** Eval the omni chip against the various comps **/
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runEval(annotate_764.out,gunzip_p1_ceu.outFile,"OMNI_764","Pilot1_CEU",pilot1_interval_list, b36_ref)
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runEval(annotate_421.out,gunzip_p1_ceu.outFile,"OMNI_421","Pilot1_CEU",pilot1_interval_list, b36_ref,true)
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//runEval(OMNI_hapmap_b36_vcf,gunzip_p1_ceu.outFile,"OMNI_421_Unfixed","Pilot1_CEU",pilot1_interval_list,b36_ref)
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runEval(annotate_764.out,gunzip_p1_chb.outFile,"OMNI_764","Pilot1_CHB",pilot1_interval_list, b36_ref)
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runEval(annotate_421.out,gunzip_p1_chb.outFile,"OMNI_421","Pilot1_CHB",pilot1_interval_list, b36_ref)
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runEval(annotate_764.out,gunzip_p1_yri.outFile,"OMNI_764","Pilot1_YRI",pilot1_interval_list, b36_ref)
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runEval(annotate_421.out,gunzip_p1_yri.outFile,"OMNI_421","Pilot1_YRI",pilot1_interval_list, b36_ref)
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runEval(annotate_764.out,pilot3_release_vcf,"OMNI_764","Pilot3",pilot3_interval_list, b36_ref)
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runEval(annotate_421.out,pilot3_release_vcf,"OMNI_421","Pilot3",pilot3_interval_list, b36_ref)
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runEval(annotate_764_b37.out,gunzip_ag_eur.outFile,"OMNI_764","August_EUR",production_interval_list, b37_ref)
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runEval(annotate_764_b37.out,gunzip_ag_asn.outFile,"OMNI_764","August_ASN",production_interval_list, b37_ref)
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runEval(annotate_764_b37.out,gunzip_ag_afr.outFile,"OMNI_764","Ausust_AFR",production_interval_list, b37_ref)
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runEval(annotate_764.out,gunzip_hiseq.outFile,"OMNI_764","HiSeq",hiseq_interval_list, b36_ref)
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runEval(annotate_764.out,annotate_421.out,"OMNI_764","OMNI_421_FIXED",pilot1_interval_list,b36_ref)
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runEval(annotate_764.out,OMNI_QUAD_1KG,"OMNI_764","OMNI_QUAD",pilot1_interval_list,b36_ref)
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runEval(annotate_764.out,AFFY_6_0,"OMNI_764","AFFY_6_0",pilot1_interval_list,b36_ref)
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runEval(OMNI_b37_birdseed,gunzip_ag_eur.outFile,"OMNI_birdseed","August_EUR",production_interval_list,b37_ref)
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runEval(OMNI_b37_joint,gunzip_ag_eur.outFile,"OMNI_joint","August_EUR",production_interval_list,b37_ref)
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runEval(OMNI_QUAD_1KG,gunzip_p1_ceu.outFile,"OMNI_QUAD_1KG","Pilot1_CEU",pilot1_interval_list,b36_ref)
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runEval(AFFY_6_0,gunzip_p1_ceu.outFile,"AFFY_6_0","Pilot1_CEU",pilot1_interval_list,b36_ref)
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var eval1KG_exclude = new VariantEval with OmniArgs
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eval1KG_exclude.samples :+= "/broad/shptmp/chartl/omni/scratch/OMNI_764_vs_Pilot3.sample_overlap.exclude.mixups.txt"
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eval1KG_exclude.rodBind :+= new RodBind("evalOMNI_764","VCF",annotate_764.out)
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eval1KG_exclude.rodBind :+= new RodBind("compPilot3","VCF",pilot3_release_vcf)
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eval1KG_exclude.evalModule :+= "GenotypeConcordance"
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eval1KG_exclude.evalModule :+= "SimpleMetricsBySample"
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eval1KG_exclude.reference_sequence = b36_ref
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eval1KG_exclude.reportType = VE2TemplateType.CSV
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eval1KG_exclude.intervalsString :+= pilot3_interval_list
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eval1KG_exclude.out = new File(eval_dir+"%s_vs_%s.%s".format("OMNI_764","Pilot3","exclude.mixups.eval.csv"))
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add(eval1KG_exclude)
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runAFComparison(annotate_764.out, gunzip_p1_ceu.outFile, gunzip_p1_chb.outFile, gunzip_p1_yri.outFile)
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var subset421: SelectVariants = new SelectVariants with OmniArgs
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subset421.reference_sequence = b36_ref
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subset421.sample :+= (new File(scratch_dir+"OMNI_421_vs_Pilot1_CEU.sample_overlap.txt")).getAbsolutePath
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subset421.variantVCF = annotate_764.out
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subset421.out = new File(vcf_dir+swapExt(annotate_764.out.getName,".vcf",".subset.pilot1CEU.vcf"))
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add(subset421)// lastly to find things in the three-way pilot venn
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var combine: CombineVariants = new CombineVariants with OmniArgs
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combine.reference_sequence = b36_ref
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combine.rodBind :+= new RodBind("CEU","VCF",gunzip_p1_ceu.outFile)
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combine.rodBind :+= new RodBind("ASN","VCF",gunzip_p1_chb.outFile)
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combine.rodBind :+= new RodBind("YRI","VCF",gunzip_p1_yri.outFile)
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combine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.UNIQUIFY
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combine.priority = "%s,%s,%s".format("CEU","ASN","YRI")
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combine.out = new File(vcf_dir+"Pilot1_Populations_Combined.vcf")
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add(combine)
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selectSites(OMNI_b36_panel_vcf,p1_ceu_only,"ceu_only_sites")
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selectSites(OMNI_b36_panel_vcf,p1_chbjpt_only,"chbjpt_only_sites")
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selectSites(OMNI_b36_panel_vcf,p1_yri_only,"yri_only_sites")
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runBeagleAnalysis(new File(vcf_dir + "Illumina_HapMap_Omni_2.5_764samples.annot.stripped.vcf"))
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}
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def processAuxiliaryChipData(otherChips: File) : List[(String,File)] = {
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// todo ==== me
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return Nil
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}
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def runEval(eval: File, comp: File, eBase: String, cBase: String, intervals: String, reference: File, interesting: Boolean = false) = {
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var base = "%s_vs_%s".format(eBase,cBase)
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var getOverlap = new GetSampleOverlap
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getOverlap.in_vcfs :+= eval
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getOverlap.in_vcfs :+= comp
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getOverlap.outFile = new File(scratch_dir+base+".sample_overlap.txt")
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add(getOverlap)
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var vEval = new VariantEval with OmniArgs
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vEval.samples :+= getOverlap.outFile.getAbsolutePath
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vEval.rodBind :+= new RodBind("eval"+eBase,"VCF",eval)
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vEval.rodBind :+= new RodBind("comp"+cBase,"VCF",comp)
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vEval.evalModule :+= "GenotypeConcordance"
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vEval.evalModule :+= "SimpleMetricsBySample"
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vEval.intervalsString :+= intervals
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vEval.reference_sequence = reference
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vEval.reportType = VE2TemplateType.CSV
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vEval.out = new File(eval_dir+base+".eval.csv")
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if ( interesting ) {
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vEval.discordantInteresting = true
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vEval.outputVCF = new File(vcf_dir+"%s_vs_%s.interesting_sites.vcf".format(eBase,cBase))
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}
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add(vEval)
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}
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def swapExt(s: String, d: String, f: String) : String = {
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return s.stripSuffix(d)+f
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}
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def runAFComparison(omni: File, p1ceu: File, p1asn: File, p1yri:File ) : Boolean = {
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// step one, set up some of the info
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var populations : List[String] = Nil // these are the pilot 1 populations
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populations :+= "CEU"
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populations :+= "CHBJPT"
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populations :+= "YRI"
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var panels : List[String] = Nil // these are the analysis panels
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panels :+= "EUR"
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panels :+= "ASN"
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panels :+= "ASW"
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panels :+= "AFR"
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panels :+= "ADM"
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// step two -- subset the OMNI chip to the actual sample names
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var nameToSubset: HashMap[String,SelectVariants] = new HashMap[String,SelectVariants]
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for ( p <- populations ) {
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nameToSubset += p -> sampleSubset(p,omni)
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}
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for ( p <- panels ) {
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nameToSubset += p -> sampleSubset(p,omni)
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}
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// step three -- compare the pilot 1 files against all populations and panels
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runComps("Pilot1CEU",p1ceu,"CEU",nameToSubset("CEU").out)
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runComps("Pilot1CEU",p1ceu,"EUR",nameToSubset("EUR").out)
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runComps("Pilot1CHBJPT",p1asn,"CHBJPT",nameToSubset("CHBJPT").out)
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runComps("Pilot1CHBJPT",p1asn,"ASN",nameToSubset("ASN").out)
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runComps("Pilot1YRI",p1yri,"YRI",nameToSubset("YRI").out)
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runComps("Pilot1YRI",p1yri,"AFR",nameToSubset("AFR").out)
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runComps("EUR",nameToSubset("EUR").out,"AFR",nameToSubset("AFR").out)
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runComps("EUR",nameToSubset("EUR").out,"ASN",nameToSubset("ASN").out)
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runComps("EUR",nameToSubset("EUR").out,"ASW",nameToSubset("ASW").out)
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runComps("EUR",nameToSubset("EUR").out,"AMR",nameToSubset("ADM").out)
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var panelCombine: CombineVariants = new CombineVariants with OmniArgs
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panelCombine.reference_sequence = b36_ref
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panelCombine.priority = ""
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for ( p <- panels ) {
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panelCombine.rodBind :+= new RodBind(p,"VCF",nameToSubset(p).out)
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panelCombine.priority = if ( panelCombine.priority.equals("") ) p else panelCombine.priority + "," + p
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}
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panelCombine.out = OMNI_b36_panel_vcf
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panelCombine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE
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panelCombine.variantMergeOptions = VariantContextUtils.VariantMergeType.UNION
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panelCombine.setKey = "panel"
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|
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add(panelCombine)
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return true
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|
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}
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|
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def getOmniSampleListByPanel(panel: String) : String = {
|
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return scratch_dir+"OMNI_764_%s.txt".format(panel)
|
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}
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|
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def sampleSubset(panel: String, omni: File) : SelectVariants = {
|
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var sv : SelectVariants = new SelectVariants with OmniArgs
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sv.reference_sequence = b36_ref
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sv.variantVCF = omni
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sv.sample :+= getOmniSampleListByPanel(panel)
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sv.out = new File(vcf_dir+swapExt(omni.getName,".vcf",".%s.vcf".format(panel)))
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add(sv)
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return sv
|
|
}
|
|
|
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def runComps(eBase: String, evalVCF: File, cBase: String, compVCF: File) = {
|
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var eval: VariantEval = new VariantEval with OmniArgs
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eval.reference_sequence = b36_ref
|
|
eval.rodBind :+= new RodBind("eval%s".format(eBase),"VCF",evalVCF)
|
|
eval.rodBind :+= new RodBind("comp%s".format(cBase),"VCF",compVCF)
|
|
eval.noStandard = true
|
|
eval.E :+= "AlleleFrequencyComparison"
|
|
eval.reportType = VE2TemplateType.CSV
|
|
eval.out = new File(eval_dir+"%s_vs_%s_allele_frequency.eval".format(eBase,cBase))
|
|
|
|
add(eval)
|
|
|
|
var combine: CombineVariants = new CombineVariants with OmniArgs
|
|
combine.reference_sequence = b36_ref
|
|
combine.rodBind :+= new RodBind(eBase,"VCF",evalVCF)
|
|
combine.rodBind :+= new RodBind(cBase,"VCF",compVCF)
|
|
combine.out = new File(vcf_dir+"%s_plus_%s.vcf".format(eBase,cBase))
|
|
combine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.UNIQUIFY
|
|
combine.priority = "%s,%s".format(eBase,cBase)
|
|
|
|
//add(combine)
|
|
|
|
}
|
|
|
|
def selectSites(vcf: File, intervals: String, base: String) {
|
|
var sv = new SelectVariants with OmniArgs
|
|
sv.reference_sequence = b36_ref
|
|
sv.variantVCF = vcf
|
|
sv.out = swapExt(vcf,".vcf",base+".vcf")
|
|
sv.intervalsString :+= intervals
|
|
|
|
add(sv)
|
|
}
|
|
|
|
def runBeagleAnalysis(omnivcf: File) {
|
|
var combine : CombineVariants = new CombineVariants with OmniArgs
|
|
combine.reference_sequence = b36_ref
|
|
for ( c <- 1 until 23) {
|
|
combine.rodBind :+= new RodBind("beagle%s".format(c),"VCF",runBeagle(omnivcf,"%s".format(c)))
|
|
if ( c > 1 ) {
|
|
combine.priority = combine.priority+",%s%s".format("beagle",c)
|
|
} else {
|
|
combine.priority = "%s%s".format("beagle",c)
|
|
}
|
|
}
|
|
combine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.PRIORITIZE
|
|
combine.variantMergeOptions = VariantContextUtils.VariantMergeType.UNION
|
|
|
|
combine.out = swapExt(pilot1_with_na12878_vcf,".vcf",".beagle_refined_with_omni.vcf")
|
|
|
|
add(combine)
|
|
|
|
var select : SelectVariants = new SelectVariants with OmniArgs
|
|
select.reference_sequence = b36_ref
|
|
select.variantVCF = combine.out
|
|
select.sample :+= "NA12878"
|
|
select.out = new File(vcf_dir + "NA12878.lowpass.beagle.refined.with.pilot1.vcf")
|
|
|
|
add(select)
|
|
|
|
var eval : VariantEval = new VariantEval with OmniArgs
|
|
eval.reference_sequence = b36_ref
|
|
eval.rodBind :+= new RodBind("evalNA12878LowPass","VCF",select.out)
|
|
eval.rodBind :+= new RodBind("compNA12878HiSeq","VCF",hiseq_calls_vcf)
|
|
eval.E :+= "GenotypeConcordance"
|
|
eval.out = new File(eval_dir+"NA12878.lowpass.beagle.vs.HiSeq.eval")
|
|
eval.excludeIntervals :+= new File(pilot1_interval_list)
|
|
eval.reportType = VE2TemplateType.CSV
|
|
|
|
add(eval)
|
|
|
|
var eval2: VariantEval = new VariantEval with OmniArgs
|
|
eval2.reference_sequence = b36_ref
|
|
eval2.rodBind :+= new RodBind("evalNA12878Beagle","VCF",pilot1_na12878_beagle)
|
|
eval2.rodBind :+= new RodBind("compNA12878HiSeq","VCF",hiseq_calls_vcf)
|
|
eval2.E :+= "GenotypeConcordance"
|
|
eval2.sample :+= "NA12878"
|
|
eval2.out = new File(eval_dir+"NA12878.lowpass.nochip.vs.Hiseq.eval")
|
|
eval2.excludeIntervals :+= new File(pilot1_interval_list)
|
|
eval2.reportType = VE2TemplateType.CSV
|
|
|
|
add(eval2)
|
|
|
|
var eval3: VariantEval = new VariantEval with OmniArgs
|
|
eval3.reference_sequence = b36_ref
|
|
eval3.rodBind :+= new RodBind("evalNA12878NoBeagle","VCF",pilot1_with_na12878_vcf)
|
|
eval3.rodBind :+= new RodBind("compNA12878HiSeq","VCF",hiseq_calls_vcf)
|
|
eval3.E :+= "GenotypeConcordance"
|
|
eval3.sample :+= "NA12878"
|
|
eval3.out = new File(eval_dir+"NA12878.lowpass.nochip.norefined.vs.Hiseq.eval")
|
|
eval3.excludeIntervals :+= new File(pilot1_interval_list)
|
|
eval3.reportType = VE2TemplateType.CSV
|
|
|
|
add(eval3)
|
|
}
|
|
|
|
def runBeagle(omnivcf: File, chr: String): File = {
|
|
var beagleInput = new ProduceBeagleInput with OmniArgs
|
|
beagleInput.reference_sequence = b36_ref
|
|
beagleInput.intervalsString :+= chr
|
|
beagleInput.variantVCF = pilot1_with_na12878_vcf
|
|
beagleInput.rodBind :+= new RodBind("validation","VCF",omnivcf)
|
|
beagleInput.validation_genotype_ptrue = 0.99
|
|
beagleInput.out = new File(scratch_dir+"/"+swapExt(beagleInput.variantVCF.getName,".vcf",".%s.beagle".format(chr)))
|
|
println (beagleInput.out.getAbsolutePath)
|
|
|
|
var runBeagle : BeagleRefinement = new BeagleRefinement
|
|
runBeagle.beagleInput = beagleInput.out
|
|
runBeagle.beagleOutputBase = "Pilot1_NA12878_Beagle_with_OMNI_chr%s".format(chr)
|
|
runBeagle.beagleMemoryGigs = 6
|
|
runBeagle.memoryLimit = 6
|
|
runBeagle.beagleOutputDir = ""
|
|
runBeagle.freezeOutputs
|
|
|
|
var gunzipPhased = new GunzipFile
|
|
gunzipPhased.gunzipMe = runBeagle.beaglePhasedFile
|
|
gunzipPhased.outFile = new File(scratch_dir+swapExt(runBeagle.beaglePhasedFile.getName,".gz",""))
|
|
|
|
var gunzipLike = new GunzipFile
|
|
gunzipLike.gunzipMe = runBeagle.beagleLikelihoods
|
|
gunzipLike.outFile = new File(scratch_dir+swapExt(runBeagle.beagleLikelihoods.getName,".gz",""))
|
|
|
|
|
|
var convertBack : BeagleOutputToVCF = new BeagleOutputToVCF with OmniArgs
|
|
convertBack.reference_sequence = b36_ref
|
|
convertBack.variantVCF = pilot1_with_na12878_vcf
|
|
convertBack.intervalsString :+= chr
|
|
convertBack.rodBind :+= new RodBind("beagleR2","beagle",runBeagle.beagleRSquared)
|
|
convertBack.rodBind :+= new RodBind("beagleProbs","beagle",gunzipLike.outFile)
|
|
convertBack.rodBind :+= new RodBind("beaglePhased","beagle",gunzipPhased.outFile)
|
|
convertBack.out = new File(vcf_dir+swapExt(pilot1_with_na12878_vcf.getName,".vcf",".chr%s.beagle_refined_plus_omni.vcf".format(chr)))
|
|
|
|
add(beagleInput,runBeagle,gunzipPhased,gunzipLike,convertBack)
|
|
|
|
return convertBack.out
|
|
}
|
|
|
|
class BeagleRefinement extends CommandLineFunction {
|
|
@Input(doc="The beagle input file") var beagleInput: File = _
|
|
var beagleOutputBase: String = _
|
|
var beagleMemoryGigs: Int = 4
|
|
|
|
/**
|
|
* Note: These get set
|
|
*/
|
|
@Output(doc="The beagle phased file") var beaglePhasedFile: File = _
|
|
@Output(doc="The beagle likelihood file") var beagleLikelihoods: File = _
|
|
@Output(doc="The beagle r2 file") var beagleRSquared: File = _
|
|
var beagleOutputDir: String = _
|
|
|
|
def freezeOutputs = {
|
|
if ( beagleOutputDir == null && beagleInput.getParent == null ) {
|
|
beagleOutputDir = ""
|
|
} else if ( beagleOutputDir == null ) {
|
|
beagleOutputDir = beagleInput.getParent+"/"
|
|
}
|
|
beaglePhasedFile = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".phased.gz")
|
|
beagleLikelihoods = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".gprobs.gz")
|
|
beagleRSquared = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".r2")
|
|
}
|
|
|
|
def commandLine = "java -Djava.io.tmpdir=%s -Xmx%dg -jar /humgen/gsa-hpprojects/software/beagle/beagle.jar like=%s out=%s".format(beagleInput.getParent,beagleMemoryGigs,beagleInput.getAbsolutePath,beagleOutputBase)
|
|
}
|
|
}
|