GATK 3.5: CRAM file error with samtools-1.3
I recently created a cram file using PrintReads and tried to view the file with samtools-1.3. The header could be viewed just fine, but after the header ended the file was considered to be truncated. I received the following error:
Failed to populate reference for id 0
Unable to fetch reference #0 10001..893888
Failure to decode slice
[main_samview] truncated file.
The cram file size seems appropriate and could even be converted back to a BAM file with PrintReads successfully. I am not sure if this is a compatibility issue and if so is there a fix in the works.