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.
Error with UnifiedGenotyper after using BaseRecalibrator twice
I am calling SNPs on an organism without a reference genome or database of known polymorphisms, so I'm trying to follow the advice posted here (and in the BaseRecalibrator documentation).
I've successfully called SNPs on the un-recalibrated .bam file, then used those SNPs to recalibrate, then called SNPs on the recalibrated .bam file. As expected, I got significantly fewer (and presumably more accurate) results.
I then used the new, reduced set of SNPs to recalibrate again. When I attempted to call SNPs on this "Round Two" recalibrated .bam file, I got the following error:
SAM/BAM file recalibrated.2.bam is malformed: Program record with group id GATK PrintReads already exists in SAMFileHeader!
I attempted to use PicardTools ValidateSamFile and CleanSam but received the same message (as an IllegalArgumentException). I would definitely consider myself a novice in the field. Any advice you can give will be greatly appreciated.