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.

BAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38)

Hi!

I am trying to perform CollectSequencingArtifactMetrics but I'm getting an error of the dictionary sizes.
Long story short, I performed BWA-MEM using hg38 in Galaxy Project (https://usegalaxy.org) and now I'm using hg38 provided in the GATK resource bundle (https://software.broadinstitute.org/gatk/download/bundle). The problem is that the header for the bam files generated from the BWA-MEM in Galaxy are different from the GATK reference genome fasta header (Homo_sapiens_assembly38.fasta).

Is there any way to solve this without remapping with GATK reference genome? Could I somehow edit the BAM header to match the GATK one?

Thanks! Joan

Best Answers

Answers

Sign In or Register to comment.