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UnifiedGenotyper error

mimi_luptonmimi_lupton Posts: 8Member

I am using UnifiedGenotyper to call SNPs in certain regions from custom capture data. I previously had the pipeline working, but now I am trying with files that have been reduced using ReduceReads, and also changed to a newer version. I have many bam files, but I also get the error when I try with just two. See below for my script and the error message.

Many thanks.

java -Xmx20g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper \ -R human_g1k_v37.fasta \ -B:dbsnp,vcf dbsnp_132.b37.vcf \ -L baitgroupfile.picard \ -I file1.reduced.bam \ -I file2.reduced.bam \ -o out.vcf \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -G Standard \ -metrics out.metrics

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

net.sf.samtools.SAMFormatException: Unrecognized tag type: B at net.sf.samtools.BinaryTagCodec.readValue(BinaryTagCodec.java:270) at net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:220) at net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:302) at net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:282) at net.sf.samtools.SAMRecord.getAttribute(SAMRecord.java:830) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:132) at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100) at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:803) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:769) at org.broadinstitute.sting.gatk.iterators.ReadFormattingIterator.next(ReadFormattingIterator.java:77) at org.broadinstitute.sting.gatk.iterators.ReadFormattingIterator.next(ReadFormattingIterator.java:19) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.(CountingFilteringIterator.java:59) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.applyDecoratingIterators(SAMDataSource.java:598) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.getIterator(SAMDataSource.java:517) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.seek(SAMDataSource.java:462) at org.broadinstitute.sting.gatk.executive.MicroScheduler.getReadIterator(MicroScheduler.java:150) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:56) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:209) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:109) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4905):
ERROR
ERROR Please visit to wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Unrecognized tag type: B
ERROR ------------------------------------------------------------------------------------------

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