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.
When should I merge results from different lanes that are from the same sample?
I have 10 exome samples run on 5 lanes (each lane has 10 samples), so essentially I have 10 FASTQ files for each sample (Lane1_R1,2 ... Lane5_R1,2). My question is should I merge from the beginning (e.g. into Lane1-5_R1,2), or should I process these individually into BAM files and merge later? If the answer is the latter, then when and how should I merge the results? The aim of the project is to find mutations. Thanks.