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.
fixmisencoded quality scores for combination of correct and incorrect encoding
When I rand Mutect on a .bam file for tumor and normal sequences, I received an error message about incorrectly encoded quality scores, so I applied the --fixencodedqualityscores and re-ran Mutect. This time, I'm getting an error message:
Bad input: while fixing mis-encoded base qualities we encountered a read that was correctly encoded; we cannot handle such a mixture of reads so unfortunately the BAM must be fixed with some other tool
Evidently, this is because one of the files (control) was correctly encoded while the other (tumor, which I had to realign) was not. Is there a flag I can use to tell Mutect to only apply the quality scores fix to one of the files while running? Otherwise, there is an entire set of control .bams that I'll need to realign just to correct this problem.