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SplitNCigarReads complains about N in CIGAR
I am working on RNAseq data. I expect SplitNCigarReads can handel spliced reads, but it complains about N in CIGAR. I just wonder whether SplitNCigarReads is ready to handle spliced reads or still under construction. I am using version 3.1-1-g07a4bf8.
The command line is "java -jar $GATKjar -T SplitNCigarReads -I a.bam -R $REFfa -o a.splitN.bam".
The error message is as follows:
MESSAGE: Unsupported CIGAR operator N in read DHT4KXP1:231:C4DW4ACXX:3:1301:3574:77410 at chrM:673. 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 are including the pertinent unsafe flag (please add -U ALLOW_N_CIGAR_READS to your command line).
According to the error message, it seems SplitNCigarReads still cannot handle spliced reads. Or, I missed something? Thanks!