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gatk4-cnn-variant-filter-azure
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Changed input data paths (#2)

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Olesya Melnichenko 2020-10-15 11:08:02 -07:00 коммит произвёл GitHub
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22
cram2filtered.inputs.json
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@ -1,24 +1,24 @@
{
"Cram2FilteredVcf.input_file": "/msgenpublicdata/inputs/cnn-sample/NA12878.cram",
"Cram2FilteredVcf.reference_fasta": "/msgenpublicdata/inputs/cnn-sample/Homo_sapiens_assembly38.fasta",
"Cram2FilteredVcf.reference_dict": "/msgenpublicdata/inputs/cnn-sample/Homo_sapiens_assembly38.dict",
"Cram2FilteredVcf.reference_fasta_index": "/msgenpublicdata/inputs/cnn-sample/Homo_sapiens_assembly38.fasta.fai",
"Cram2FilteredVcf.input_file": "/datasettestinputs/dataset/gatk4-cnn-variant-filter/NA12878.cram",
"Cram2FilteredVcf.reference_fasta": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta",
"Cram2FilteredVcf.reference_dict": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.dict",
"Cram2FilteredVcf.reference_fasta_index": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"Cram2FilteredVcf.resources": [
"/msgenpublicdata/inputs/cnn-sample/hapmap_3.3.hg38.vcf.gz",
"/msgenpublicdata/inputs/cnn-sample/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"/msgenpublicdata/inputs/cnn-sample/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
"/datasettestinputs/dataset/references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"/datasettestinputs/dataset/references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"/datasettestinputs/dataset/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
],
"Cram2FilteredVcf.resources_index": [
"/msgenpublicdata/inputs/cnn-sample/hapmap_3.3.hg38.vcf.gz.tbi",
"/msgenpublicdata/inputs/cnn-sample/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"/msgenpublicdata/inputs/cnn-sample/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"
"/datasettestinputs/dataset/references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
"/datasettestinputs/dataset/references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"/datasettestinputs/dataset/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"
],
"Cram2FilteredVcf.output_prefix": "hg38_20k_na12878",
"Cram2FilteredVcf.info_key": "CNN_2D",
"Cram2FilteredVcf.snp_tranches": " --snp-tranche 99.9 ",
"Cram2FilteredVcf.indel_tranches": " --indel-tranche 99.5 ",
"Cram2FilteredVcf.tensor_type": "read_tensor",
"Cram2FilteredVcf.calling_intervals": "/msgenpublicdata/inputs/cnn-sample/wgs_calling_regions.hg38.interval_list",
"Cram2FilteredVcf.calling_intervals": "/datasettestinputs/dataset/references/hg38/v0/wgs_calling_regions.hg38.interval_list",
"Cram2FilteredVcf.gatk_docker": "broadinstitute/gatk:4.1.4.0",
"Cram2FilteredVcf.preemptible_attempts": 10,
"Cram2FilteredVcf.inference_batch_size": 8,