I have a bam file with duplicates removed. And I added the read groups using picard as:
java -jar gatk/picard-tools-2.5.0/picard.jar AddOrReplaceReadGroups \
I=input.bam \
O=input.group.bam \
RGID=4 \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=20
Then I run the HaplotypeCaller
java -jar gatk/GenomeAnalysisTK.jar -T HaplotypeCaller \
-R /hg19/ucsc.hg19.fasta \
-I input.group.bam \
--dbsnp snps.vcf \
-o input.raw.vcf
But I get the following error:
java.lang.NumberFormatException: empty String
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.valueOf(Double.java:502)
at htsjdk.variant.vcf.AbstractVCFCodec.parseQual(AbstractVCFCodec.java:511)
at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:317)
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:74)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:36)
at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:493)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.(IndexFactory.java:394)
at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:303)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:441)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:327)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:264)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:153)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:1047)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:824)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:282)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
Can you help about this problem? Thanks.