Print Reads in GATK
I am unable to execute 'Print Reads' as I get the following error:
Unsupported CIGAR operator N in read read704 at chr21:33029208. Perhaps you are trying to use
RNA-Seq data? While we are currently actively working to support this data type unfortunately
the GATK cannot be used with this data in its current form. You have the option of either
filtering out all reads with operator N in their CIGAR string(please add --
filter_reads_with_N_cigar to your command line) or assume the risk of processing those reads as
they arre including the pertinent unsafe flag(please add -U ALLOW_N_CIGAR_READS to your command
line). Notice however that if you were to choose the latter, an unspecified subset of the
analytical outputs of an unspecified subset of the tools will become unpredictable. Consequently
the GATK team might well not be able to provide you with the usual support with any issue
regarding any output.
I tried both ways of filter option and allow cigar reads....but I still have the same error. Can you please help me in resolving this as soon as you can?
Thanks and Regards