I was using PrintReads as part of Base Quality Recalibration. The resulting BAM header is incorrect as there are two @PG entries for GATK PrintReads. The bam file I am using is internal to the broad institute and is picard aggregated. There is an entry for GATK PrintReads in the original bam. Would it be possible for the @PG header lines to include a .A-Z like the other headers?
ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: SAM/BAM file /btl/projects/aaron/Mouse/G42214/TET-OT-827ctl.recalibrated.bam is malformed: Program record with group id GATK PrintReads already exists in SAMFileHeader!