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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.

Where do the test files reside for the dockerstore.org workflows?

rdbremelrdbremel Madison WIMember

**e.g.
JSON for RNAseq

rna-germline-variant-calling

the files are not FTPable and are not in the "bundle" directories
**

{
"##_COMMENT1": "Input",
"RNAseq.inputBam": "gs://gatk-test-data/rna_bam/NA12878_b37/NA12878.bam",

"##_COMMENT2": "REFERENCE FILES",
"RNAseq.refFasta": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta",
"RNAseq.refFastaIndex": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai",
"RNAseq.refDict": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dict",

"##_COMMENT3": "INTERVALS",
"RNAseq.wgsCallingIntervalList": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.whole_genome.interval_list",

"##_COMMENT4": "RESOURCE FILES",
"RNAseq.dbSnpVcf": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf",
"RNAseq.dbSnpVcfIndex": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf.idx",
"RNAseq.knownVcfs": [
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf",
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf"
],
"RNAseq.knownVcfsIndices": [
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx",
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf.idx"
],
"RNAseq.annotationsGTF": "gs://gatk-test-data/intervals/star.gencode.v19.transcripts.patched_contigs.gtf",

"##_COMMENT4": "DOCKERS",
"#RNAseq.gatk4_docker_override": "String? (optional)",
"#RNAseq.star_docker_override": "String? (optional)",
"#RNAseq.gitc_docker_override": "String? (optional)",

"##_COMMENT5": "PATHS",
"#RNAseq.gatk_path_override": "/gatk/gatk",

"##_COMMENT6": "PREEMPTIBLES",
"##RNAseq.preemptible_tries": "(optional) Int?",

"##_COMMENT7": "Misc",
"#RNAseq.StarAlign.num_threads": "(optional) Int?",
"#RNAseq.StarAlign.star_limitOutSJcollapsed": "(optional) Int?",
"RNAseq.StarAlign.additional_disk": "50",
"#RNAseq.StarAlign.star_mem_max_gb": "(optional) Int?",
"RNAseq.StarGenerateReferences.addtional_disk": 50,
"#RNAseq.StarGenerateReferences.num_threads": "(optional) Int?",
"#RNAseq.StarGenerateReferences.mem_gb": "(optional) Int?",
"#RNAseq.haplotypeScatterCount": "(optional) Int?",
"#RNAseq.use_gatk4_for_all_tools": "(optional) Boolean",
"#RNAseq.minConfidenceForVariantCalling": "(optional) Int?",
"#RNAseq.zippedStarReferences": "(optional) File?",
"#RNAseq.readLength": "(optional) Int?"
}

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