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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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