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.
Realigning sample-merged bam files?
Following GATK's best practices, I have individually realigned/recalibrated my sample-lane bams and merged them by sample:
sample1_lane2.dedup.realn.recal.bam --> sample1.merged.bam
sample2_lane2.dedup.realn.recal.bam --> sample2.merged.bam
I am ready to dedup and realign my sample merged bams, however I am uncertain on the best approach. Is the consensus to convert back to fastq via Picard (MarkDuplicates, SortSam, and SamToFastq) and then run bwa mem? Or is it more expedient/accurate to realign the sample-merged bam using bwa aln followed by bwa sampe?