CRAMs generated by GATK don't always have M5/UR attributes in the sequence dictionary
open | Created 2018-09-17 | Last updated 2018-09-17| Posted by cmnbroad | See in Github


See samtools/htslib#769 (comment). These are requried by the CRAM spec, but htsjdk-generated files will only have them if they appear in the input/source dictionary from which the CRAM was generated. The fix should be in htsjdk see samtools/htsjdk#506.

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