Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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