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Bug with read clipper and fix_misencoded_quality_scores option
I was softclipping some 84-bp-long single end reads using the following command:
java -Xmx2g -jar /GATK_Path/GenomeAnalysisTK.jar -T ClipReads -I imput_file.bam -o output_file.bam -R $ALIGNREF --cyclesToTrim "1-4,80-84" --clipRepresentation SOFTCLIP_BASES --fix_misencoded_quality_scores
There was no error while running, but when I looked at the file afterwards, every read had a cigar string of 84S. I'm fairly sure this is a bug. I was aligned to the human mitochondrial genome.
I am using GATK v2.3-9-ge5ebf34 on Mac OS 10.75