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.
Implementing your workflows from git repository to run locally
First of all, thanks a lot for putting up those GATK workflows. As a non-bioinformatician at the core, I truly appreciate those shortcuts!
And this question comes right after I performed your first tutorial on workflows, and now I want to explore more of them.
I was particularly interested in starting by your "cnn-variant-filter", after reading about it here.
So, I pull the workflow and went straight to change its json file (
cram2filtered.inputs.json). First thing I notice is that all paths are set to
gs://. And second was that there are a lot of inputs that I don't know where to retrieve them. More specifically these lines:
"Cram2FilteredVcf.reference_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", "Cram2FilteredVcf.reference_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict", "Cram2FilteredVcf.reference_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", "Cram2FilteredVcf.resource_fofn": "gs://gatk-best-practices/cnn-h38/resource_fofn.txt", "Cram2FilteredVcf.resource_fofn_index": "gs://gatk-best-practices/cnn-h38/resource_fofn_index.txt", "Cram2FilteredVcf.calling_intervals": "gs://broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list"
Another thing is that the workflow is set to run by using a
.cram file as input. In my case, I would like to use
BAI as inputs.
That being said, how could I implement this to run locally and using BAM and BAI files as inputs? Would using the gatk docker help here? If so, how would I use it?
Any help is very much appreciated!