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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
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
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