Dear GATK Team,
When running IlluminaBasecallsToSam, I submit a LIBRARY_PARAMS file with the following headers, with the aim of a different ID being inserted into the RG header and tag per read group and therefore, per uBAM generated:
SAMPLE_ALIAS LIBRARY_NAME BARCODE_1 OUTPUT ID
However, although the ID I have specified is inserted into the header of each uBAM file generated per read group, this is in addition to an automated ID generated by IlluminaBasecallsToSam, leading to two ID fields per uBAM header.
The automated RGID is inserted into every uBAM header and tag and is the same in each uBAM. However, the ID I have specified in LIBRARY_PARAMS is unique to each uBAM but only inserted in the header. This leads to an error with ValidateSamFile and downstream processes.
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Error Type Count
How do I replace the automated ID set by IlluminaBasecallsToSam to ensure that only one RGID is inserted per read group but also ensuring it is the RGID set in the LIBRARY_PARAMS file, unique per read group?
I am using Picard version 2.23.8. The IlluminaBasecallsToSam option READ_GROUP_ID is currently set at ‘null’ and therefore, I suspect this could be contributing to the issue. However, due to having more than one read group, I do not know how to instruct READ_GROUP_ID to refer to the LIBRARY_PARAMS file and set one unique ID per read group.
Thank you for your time and help.
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