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.
VQSLOD score different for Full and split (by chromosome) BAM file
I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score:
For full : VQSLOD=-6.339e-01
For split : VQSLOD=-1.472e+00
Does this means splitting the BAM is not correct or is it because of wrong parameters? or it is correct and I can neglect this?