To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

UnifiedGenotyper error

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(
at net.sf.samtools.BinaryTagCodec.readTags(
at net.sf.samtools.BAMRecord.decodeAttributes(
at net.sf.samtools.BAMRecord.getAttribute(
at net.sf.samtools.SAMRecord.getAttribute(
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource$
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource$
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.(
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.applyDecoratingIterators(
at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.getIterator(
at org.broadinstitute.sting.gatk.executive.MicroScheduler.getReadIterator(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4905):
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
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Unrecognized tag type: B
ERROR ------------------------------------------------------------------------------------------

Best Answer


Sign In or Register to comment.