SplitNCigarReads exception

[Lien]

Hi all,

I'm trying to use the GATK pipeline for analyzing RNA-seq data and to detect variants. According to the GATK Best Practices, I need to allow reads for N cigars.
So I tried
java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R /human_g1k_v37.fasta -I Sample.dedupped.bam -o split.bam -U ALLOW_N_CIGAR_READS

I started working with version 3.2.2. This works fine for a while, until it comes to a certain line in the BAM-file and spits out this error:
Bad input: Cannot split this read (might be an empty section between Ns, for example 1N1D1N): 77M54369N2D79N24M

I looked around on the internet and found that it helps sometimes to add -fixNDN to the command. But this results in the following error:
Message: Code exception.

Futhermore, it could be a bug, so I installed the latest version of GATK (3.3.0) but I get the exact same errors (both with and without -fixNDN).

Any suggestions are most welcomed!
Thanks,
Lien

[linusvanpelt]

Hi,

I think I run into this issue the other day, too. Try the latest nightly build of GATK. That fixed it for me. This is a bug that has been fixed if I recall it right.

Cheers

[Lien]

Indeed, the latest build fixed it.