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
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ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
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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!
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