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troubles with BAM files generated by Mutect2 and FilterAlignmentArtifacts
I am using GATK 220.127.116.11 and noticed the following : if Mutect2 is run with parameter --bam-output it makes a BAM file that contains :
(note the typo)
If then FilterAlignmentArtifacts is run with this file as input and BAM output is asked, it says
java.lang.IllegalArgumentException: Program record with group id HalpotypeBAMWriter already exists in SAMFileHeader!
and does not create the file