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Fixed issues where overlapping indels having same start coordinates c…
…ounted as same
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| package gatkUtils; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.util.Iterator; | ||
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| import org.apache.commons.io.FilenameUtils; | ||
| import org.json.simple.JSONArray; | ||
| import org.json.simple.JSONObject; | ||
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| public class GatkThread implements Runnable { | ||
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| @Override | ||
| public void run() { | ||
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| JSONArray stepsArray = GatkUtils.readConfigJson(GatkUtils.configPath); | ||
| Iterator iter = stepsArray.iterator(); | ||
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| String inputFileNameNoExt = FilenameUtils.getBaseName(GatkUtils.inputBam.getFileName().toString()); | ||
| Path inputFileLocation = GatkUtils.inputBam.getParent(); | ||
| String origInputFileName = GatkUtils.inputBam.getFileName().toString(); | ||
| System.out.println(inputFileNameNoExt); | ||
| System.out.println(inputFileLocation); | ||
| System.out.println(origInputFileName); | ||
| // run sort on input file | ||
| String stepFileName = inputFileNameNoExt + ".sorted.bam"; | ||
| String listFileName = ""; | ||
| String recalGrpFile = ""; | ||
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| String command = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " + GatkUtils.maxHeapSpace + " -jar " | ||
| + GatkUtils.picardPath + " SortSam " + " SO=coordinate " + " I=" + GatkUtils.inputBam + " O=" | ||
| + inputFileLocation.resolve(stepFileName); | ||
| // System.out.println(command); | ||
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| Runtime r = Runtime.getRuntime(); | ||
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| try { | ||
| Process p2 = r.exec(command); | ||
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| StreamGobbler errGobler = new StreamGobbler(p2.getErrorStream(), "ERROR"); | ||
| StreamGobbler opGobler = new StreamGobbler(p2.getInputStream(), "OUTPUT"); | ||
| errGobler.start(); | ||
| opGobler.start(); | ||
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| p2.waitFor(); | ||
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| } catch (IOException | InterruptedException e1) { | ||
| // TODO Auto-generated catch block | ||
| e1.printStackTrace(); | ||
| } | ||
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| while (iter.hasNext()) { | ||
| JSONObject obj1 = (JSONObject) iter.next(); | ||
| System.out.println(obj1.keySet().contains("MarkDuplicates") && ((JSONObject)obj1.get("MarkDuplicates")).values().contains("true") ); | ||
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| if (obj1.keySet().contains("MarkDuplicates") && ((JSONObject)obj1.get("MarkDuplicates")).values().contains("true")) { | ||
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| String newStepFileName = inputFileLocation.resolve(FilenameUtils.getBaseName(stepFileName)).toString() | ||
| + ".mdup.bam"; | ||
| String mdupCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " + GatkUtils.maxHeapSpace | ||
| + " -jar " + GatkUtils.picardPath + " MarkDuplicates " + " I=" | ||
| + inputFileLocation.resolve(stepFileName) + " O=" + inputFileLocation.resolve(newStepFileName) | ||
| + " M=" + inputFileLocation.resolve(newStepFileName + ".metricFile") | ||
| + " VALIDATION_STRINGENCY=LENIENT"; | ||
| System.out.println(mdupCommand); | ||
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| runAndGobbleCommand(mdupCommand, r); | ||
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| stepFileName = newStepFileName; | ||
| } else if (obj1.keySet().contains("BuildBamIndex")) { | ||
| String bamIndexCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " | ||
| + GatkUtils.maxHeapSpace + " -jar " + GatkUtils.picardPath + " BuildBamIndex " + " I=" | ||
| + inputFileLocation.resolve(stepFileName); | ||
| System.out.println(bamIndexCommand); | ||
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| runAndGobbleCommand(bamIndexCommand, r); | ||
| } else if (obj1.keySet().contains("RealignerTargetCreator")) { | ||
| listFileName = inputFileLocation.resolve(FilenameUtils.getBaseName(stepFileName)).toString() + ".list"; | ||
| String realignerCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " | ||
| + GatkUtils.maxHeapSpace + " -jar " + GatkUtils.gatkPath + " -T RealignerTargetCreator " | ||
| + " -R " + GatkUtils.referencePath + " -I " + inputFileLocation.resolve(stepFileName) + " -o " | ||
| + inputFileLocation.resolve(listFileName); | ||
| System.out.println(realignerCommand); | ||
| runAndGobbleCommand(realignerCommand, r); | ||
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| } else if (obj1.keySet().contains("IndelRealigner")) { | ||
| String newStepFileName = inputFileLocation.resolve(FilenameUtils.getBaseName(stepFileName)).toString() | ||
| + ".realigned.bam"; | ||
| String indelRealignerCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " | ||
| + GatkUtils.maxHeapSpace + " -jar " + GatkUtils.gatkPath + " -T IndelRealigner " + " -R " | ||
| + GatkUtils.referencePath + " -I " + inputFileLocation.resolve(stepFileName) + " -o " | ||
| + inputFileLocation.resolve(newStepFileName) + " -targetIntervals " | ||
| + inputFileLocation.resolve(listFileName); | ||
| System.out.println(indelRealignerCommand); | ||
| runAndGobbleCommand(indelRealignerCommand, r); | ||
| stepFileName = newStepFileName; | ||
| } | ||
|
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| else if (obj1.keySet().contains("FixMateInformation")) { | ||
| // java -Xmx1g -jar | ||
| // tools\picard-tools-1.82\picard-tools-1.82\FixMateInformation.jar | ||
| // INPUT=%sampleName%.sorted.realigned.bam | ||
| // OUTPUT=%sampleName%.sorted.realigned.fixed.bam SO=coordinate | ||
| // VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true | ||
| String newStepFileName = inputFileLocation.resolve(FilenameUtils.getBaseName(stepFileName)).toString() | ||
| + ".fixed.bam"; | ||
| String mateFixCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " + GatkUtils.maxHeapSpace | ||
| + " -jar " + GatkUtils.picardPath + " FixMateInformation " + " I=" | ||
| + inputFileLocation.resolve(stepFileName) + " O=" + inputFileLocation.resolve(newStepFileName) | ||
| + " VALIDATION_STRINGENCY=LENIENT"; | ||
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| runAndGobbleCommand(mateFixCommand, r); | ||
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| stepFileName = newStepFileName; | ||
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| } else if (obj1.keySet().contains("BaseRecalibrator")) { | ||
| recalGrpFile = inputFileLocation.resolve(FilenameUtils.getBaseName(stepFileName)).toString() | ||
| + ".recal.grp"; | ||
| String baseRecalCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " | ||
| + GatkUtils.maxHeapSpace + " -jar " + GatkUtils.gatkPath + " -T BaseRecalibrator " + " -R " | ||
| + GatkUtils.referencePath + " -I " + inputFileLocation.resolve(stepFileName) + " -o " | ||
| + inputFileLocation.resolve(recalGrpFile) + " -bqsrBAQGOP 40 "; | ||
| runAndGobbleCommand(baseRecalCommand, r); | ||
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| } else if (obj1.keySet().contains("PrintReads")) { | ||
| // java -Xmx1g -jar tools\GenomeAnalysisTK.jar -T PrintReads -R %genomeRef% -I | ||
| // %sampleName%.sorted.realigned.fixed.bam -BQSR %sampleName%.recal.grp -o | ||
| // %sampleName%.sorted.realigned.fixed.bqsr.bam | ||
| String newStepFile = inputFileLocation.resolve(FilenameUtils.getBaseName(stepFileName)).toString() | ||
| + ".bqsr.bam"; | ||
| String printReadCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " | ||
| + GatkUtils.maxHeapSpace + " -jar " + GatkUtils.gatkPath + " -T PrintReads " + " -R " | ||
| + GatkUtils.referencePath + " -I " + inputFileLocation.resolve(stepFileName) + " -o " | ||
| + inputFileLocation.resolve(newStepFile) + " -BQSR " + inputFileLocation.resolve(recalGrpFile); | ||
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| runAndGobbleCommand(printReadCommand, r); | ||
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| stepFileName = newStepFile; | ||
| } else if (obj1.keySet().contains("UnifiedGenotyper")) { | ||
| // java -Xmx1g -jar tools\GenomeAnalysisTK.jar -R %genomeRef% -T | ||
| // UnifiedGenotyper -I %sampleName%.sorted.realigned.fixed.bqsr.bam -mbq 13 -glm | ||
| // BOTH -indelGCP 20 -indelGOP 40 -o %sampleName%_snps.raw.vcf -L %targetBed% | ||
| String resultVcf = inputFileLocation.resolve(inputFileNameNoExt + ".raw.vcf").toString(); | ||
| String UnifiedGenotyperCommand = "C:\\Program Files\\Java\\jdk1.8.0_192\\bin\\java.exe " | ||
| + GatkUtils.maxHeapSpace + " -jar " + GatkUtils.gatkPath + " -T UnifiedGenotyper " + " -R " | ||
| + GatkUtils.referencePath + " -I " + inputFileLocation.resolve(stepFileName) + " -o " | ||
| + inputFileLocation.resolve(resultVcf) + " -BQSR " + inputFileLocation.resolve(recalGrpFile) | ||
| + " -mbq 13 -glm BOTH -indelGCP 20 -indelGOP 40 " + " -L " + GatkUtils.targetBedFile; | ||
| runAndGobbleCommand(UnifiedGenotyperCommand, r); | ||
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| } | ||
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| } | ||
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| } | ||
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| public void runAndGobbleCommand(String command, Runtime r) { | ||
| try { | ||
| Process p2 = r.exec(command); | ||
| new StreamGobbler(p2.getErrorStream(), "ERROR").start(); | ||
| new StreamGobbler(p2.getInputStream(), "INPUT").start(); | ||
| p2.waitFor(); | ||
| } catch (IOException | InterruptedException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| } | ||
|
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| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| package gatkUtils; | ||
|
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| import java.io.File; | ||
| import java.io.FileNotFoundException; | ||
| import java.io.FileReader; | ||
| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
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| import org.json.simple.JSONArray; | ||
| import org.json.simple.parser.JSONParser; | ||
| import org.json.simple.parser.ParseException; | ||
|
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| public class GatkUtils { | ||
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| public static File logFile = new File("D:\\SureCall\\SureCall4111\\GATKcomparison\\Autommation\\gatkProcess.log"); | ||
| public static Path configPath = Paths.get("D:\\SureCall\\SureCall4111\\GATKcomparison\\Autommation\\config.json"); | ||
| //public static Path javaPath = Paths.get("java"); | ||
| public static Path gatkPath = Paths.get("D:\\SureCall\\SureCall4111\\GATKcomparison\\tools\\GenomeAnalysisTK.jar"); | ||
| public static Path picardPath = Paths.get("D:\\SureCall\\SureCall4111\\GATKcomparison\\tools\\picard.jar"); | ||
| public static String maxHeapSpace = "-Xmx4g"; | ||
| public static Path inputBam = Paths.get("D:\\SureCall\\SureCall4111\\GATKcomparison\\L004_I003_chr22_child.bam"); | ||
| public static Path referencePath = Paths.get("D:\\SureCall\\SURECALL_VALID\\Surecall_Test_plans\\Genomeanalysis_softwares\\IGV\\IGVTools\\hg19\\hg19.fasta"); | ||
| public static Path targetBedFile = Paths.get("D:\\SureCall\\SureCall4111\\GATKcomparison\\targets_subset_Exons.bed"); | ||
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| public static void main(String args[]) throws IOException { | ||
| readConfigJson(Paths.get("D:\\SureCall\\SureCall4111\\GATKcomparison\\Autommation\\config.json")); | ||
| if(logFile.createNewFile()) { | ||
| System.out.println("Created file successfully !!"); | ||
| } | ||
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| Thread th = new Thread(new GatkThread()); | ||
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| th.start(); | ||
| } | ||
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| public static JSONArray readConfigJson(Path configPath) { | ||
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| JSONParser jsonParser = new JSONParser(); | ||
| JSONArray gatkSteps = null; | ||
| try (FileReader reader = new FileReader(configPath.toFile())) | ||
| { | ||
| //Read JSON file | ||
| Object obj = jsonParser.parse(reader); | ||
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| gatkSteps = (JSONArray) obj; | ||
| // System.out.println(gatkSteps); | ||
|
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| } catch (FileNotFoundException e) { | ||
| e.printStackTrace(); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| } catch (ParseException e) { | ||
| e.printStackTrace(); | ||
| } | ||
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| return gatkSteps; | ||
| } | ||
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| } |
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