GATK still does not support cigar N from tophat?
Dear all,
I'm using GATK version 1.2-60-g585a45b to call SNV from bam file of tophat.
The first two steps, RealignerTargetCreator and IndelRealigner are good. Then on SomaticIndelDetector, I encountered an error message:
java.lang.IllegalArgumentException: Unexpected operator in cigar string: N
It seems GATK cannot deal with cigar N? Then how to run it follow tophat alignment? I really do not want to filter out those alignment with cigar N, or I manually split them into two alignments?
Any advise will be appreciated!
Mark
I'm using GATK version 1.2-60-g585a45b to call SNV from bam file of tophat.
The first two steps, RealignerTargetCreator and IndelRealigner are good. Then on SomaticIndelDetector, I encountered an error message:
java.lang.IllegalArgumentException: Unexpected operator in cigar string: N
It seems GATK cannot deal with cigar N? Then how to run it follow tophat alignment? I really do not want to filter out those alignment with cigar N, or I manually split them into two alignments?
Any advise will be appreciated!
Mark