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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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Does the best practice pipeline for pre-data processing output a merged BAM file?
I'm using the GATK4 best practice pipeline for pre-data processing. I have several questions and would like to confirm:
The final output is a merged BAM file, right? All the input per-sample BAM files are merged during
MarkDuplicatesand are processed together ever since.
It seems that I can use
SplitSamon the final output to extract the BAM files for each sample, is this correct?
In the accompanying
NA12878. Are there any special reasons for choosing this name? Or can it be any name?
Also following the 1st question, why all the input BAM files are merged? Are there any special reasons for doing so? For the dataset I'm analyzing, each BAM is about 15GB, and I have 200 such files, if they are merged together it will be 3000GB = 3TB. Although I'm using a server, still it will be very difficult to process such a huge file (if such a huge file could be supported)! Besides, since they are merged, we will not be able to have parallel computing, and the computing time will be longer.
Thank you very much for your help!