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.
merge multi-sample bam files
I have with me 1000 samples that were pooled together in 5 different libraries and sequenced for genomic regions. So first, for each library, I independantly performed alignment, marked duplicates,realigned the bam files and also did recalibration and separated the bam file for each individual. Now I have 1000 individual bam files and I wanted to check the target coverage and perform variant calling.
I wanted to know if it makes sense to merge the bam files according to cases:controls and perform the analysis with 2 bam files or is it better to carry on with single individual bam files ?