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.
the importance of sorting markduplicate output files
I discovered that several outputfiles from "markduplicates" (picard) was sent on in the "best-practice workflow (GATK4.1) " without sorting through BaseRecalibrator, BQSR (gatk ApplyBQSR) and Haplotypecaller to make g.vcf files of each sample. No obvious problems or error msg. The plan is to combine these one in a common vcf-file for variant calling. Is there a need to rerun and get these samples (coordinate) sorted after markduplicates and then rerun BaseRecalibrator, ApplyBQSR and Haplotypecallerto avoid errors?