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# Error when running UG: Unexpected base in allele bases

Cambridge, MAMember
edited August 2012

Hi,
I got the following error when running UG (on unstable from 2012/08/15, v2.0-222-gc178076)

java.lang.IllegalArgumentException: Unexpected base in allele bases 'T^@'
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.0-222-gc178076):


The arguments were something like this (modified here for readability)
Program Args: -T UnifiedGenotyper -I My.bam.list -L scatter.intervals -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta -dcov 60 -glm BOTH -capMaxAltAllelesForIndels -D /humgen/gsa-pipeline/resources/b37/v4/dbsnp_135.b37.vcf -o My.unfiltered.vcf

I put the bams and actual logs etc on the local disk at the Broad:
/xchip/cga2/akiezun/forSharing/UnexpectedBaseErrorI

I also saw the same error (modulo the precise message) on many of my other UG runs that all use the same build 2.0-222-gc178076

Tagged:

Thanks for reporting this Adam. It doesn't seem like this error should be possible with a well-formed bam, but I'd be happy to look into it. Unfortunately, I don't have read access to any of the bams in your bam list, so I'll need a little help from you. Can you please isolate the issue to small interval and then run PrintReads on that interval with your bam list, printing out to a location that I can read? I'll then take it from there.
Thanks!

• Cambridge, MAMember

Thanks for your response. I just sent the small testcase by email.

• Member

Hi, just wanted to say I got a similar error trying to SomaticIndelCaller with GATK v2.1-5

##### ERROR stack trace
java.lang.IllegalArgumentException: Unexpected base in allele bases '65C'
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