Although it does appear that the file in question was processed by MarkDuplicates, I don't think thats how the CRAM was produced. The htsjdk code doesn't implement reference-less compression (and I also don't see any code paths where it generates 'b' features). More importantly, the command line breadcrumb in the header contains no REFERENCE arg (which htsjdk would require to write a CRAM), and also indicates that the user requested that the OUTPUT of MarkDuplicates was a ".bam":
OUTPUT=fastq/DM_19_0434/GRCh37.p13/alignments/bwa/CGEN/raw_sorted_duplicates_removed.bam So I suspect the conversion to CRAM was done after the fact. -Chris
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