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modifying the processing-for-variant-discovery...inputs.json

Dear GATK Team,

I just successfully converted my fastq files to ubam and wanted to do a local data preprocessing using the uBAM to analysis-ready BAM universal pipeline.
I realized that I have to call the wdl file using the json file as an input.

I have some questions about editing the json file:

I. how should the flowcell_unmapped_bams_list be formatted? I have no access to the example "NA12878_24RG_small.txt"

II. I was able to download the “gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta” from the Resource Bundle under the Download section. Regarding the ones that end with, amb, bwt, ann, pac. I was not able to find those in the Resource Bundle on the homepage.

III. I was able to place the paths for picard and gatk. But what is gotc? ("PreProcessingForVariantDiscovery_GATK4.gotc_path": "/usr/gitc/")

IV. There are options like GATK4.agg_small_disk, medium disk and large disk. Where do I choose that the program should run on a specific size?

V. I installed gatk locally using the gatkcondaev.yml without the need of docker? Can I run the whole pipeline without docker? The json file has some options called DOCKERS.

Thanks for your help



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