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* README.md * Update to gatk4.1 * Updated forum links in Readme * changed ref file VM path to google bucket path * updated import link to git tag url * updated to GATK4.1.1.0 * minor edits * changed import to dev for pon * updated filter bias variable * updated filter bias variable * updated output variable names, removed artifact_mode from normal-normal * changed index to idx * removed artifact_modes * updated import to next release: 2.4.0 * specified gatk version in readme * Added Funcotator note to readme * Update to gatk4.1.2.0 * updated input variable for mutect2 * correctin to input vairalbe * correction to output variable * corrected variable name and simplified json
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bshifaw
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Aug 19, 2019
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| { | ||
| "##_COMMENT1": "Inputs", | ||
| "Mutect2_Panel.normal_reads": "Array[File]", | ||
| "Mutect2_Panel.normal_reads_index": "Array[File]", | ||
| "Mutect2_Panel.pon_name": "String", | ||
| "#Mutect2_Panel.Mutect2.normal_bam": "(optional) File?", | ||
| "#Mutect2_Panel.Mutect2.normal_bai": "(optional) File?", | ||
| "##_COMMENT1": "Inputs", | ||
| "Mutect2_Panel.pon_name":"panel_of_normal", | ||
| "Mutect2_Panel.normal_bams":"Array[File]", | ||
| "Mutect2_Panel.normal_bais":"Array[File]", | ||
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| "##_COMMENT2": "Primary resources", | ||
| "Mutect2_Panel.ref_fasta":"gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta", | ||
| "Mutect2_Panel.ref_fai":"gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai", | ||
| "Mutect2_Panel.ref_dict":"gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict", | ||
| "Mutect2_Panel.scatter_count":10, | ||
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| "##_COMMENT2": "Primary resources", | ||
| "Mutect2_Panel.ref_fasta": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta", | ||
| "Mutect2_Panel.ref_fai": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai", | ||
| "Mutect2_Panel.ref_dict": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict", | ||
| "Mutect2_Panel.scatter_count": "10", | ||
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| "##_COMMENT3": "Secondary resources", | ||
| "Mutect2_Panel.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list", | ||
| "##_Mutect2_Panel.Mutect2.data_sources_tar_gz": "(optional) String?", | ||
| "Mutect2_Panel.Mutect2.variants_for_contamination": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf", | ||
| "##_Mutect2_Panel.Mutect2.variants_for_contamination_index": "(optional) File?", | ||
| "##_Mutect2_Panel.Mutect2.tumor_sequencing_artifact_metrics": "(optional) File?", | ||
| "Mutect2_Panel.Mutect2.gnomad": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf", | ||
| "##_Mutect2_Panel.Mutect2.gnomad_index": "(optional) File?", | ||
| "##_Mutect2_Panel.Mutect2.onco_ds_tar_gz": "(optional) File?", | ||
| "##_Mutect2_Panel.Mutect2.pon": "(optional) File?", | ||
| "##_Mutect2_Panel.Mutect2.pon_index": "(optional) File?", | ||
| "##_Mutect2_Panel.Mutect2.default_config_file": "(optional) File?", | ||
| "##_Mutect2_Panel.gatk_override": "(optional) File?", | ||
| "##_COMMENT4": "Secondary resources", | ||
| "Mutect2_Panel.intervals":"gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list", | ||
| "Mutect2_Panel.Mutect2.variants_for_contamination":"gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf", | ||
| "Mutect2_Panel.gnomad":"gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf", | ||
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| "##_COMMENT4": "Secondary resources", | ||
| "#Mutect2_Panel.duplicate_sample_strategy": "(optional) String?", | ||
| "#Mutect2_Panel.m2_extra_args": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.onco_ds_local_db_dir": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.annotation_defaults": "(optional) Array[String]?", | ||
| "#Mutect2_Panel.Mutect2.reference_version": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.annotation_oventerrides": "(optional) Array[String]?", | ||
| "Mutect2_Panel.Mutect2.artifact_modes": ["G/T", "C/T"], | ||
| "#Mutect2_Panel.Mutect2.sequence_source": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.transcript_selection_list": "(optional) Array[String]?", | ||
| "#Mutect2_Panel.Mutect2.split_intervals_extra_args": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.sequencing_center": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.transcript_selection_mode": "(optional) String?", | ||
| "#Mutect2_Panel.Mutect2.m2_extra_filtering_args": "(optional) String?", | ||
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| "##_COMMENT5": "Boolean Options", | ||
| "#Mutect2_Panel.Mutect2.run_oncotator": "(optional) Boolean?", | ||
| "#Mutect2_Panel.Mutect2.make_bamout": "(optional) Boolean?", | ||
| "#Mutect2_Panel.Mutect2.run_funcotator": "(optional) Boolean?", | ||
| "#Mutect2_Panel.Mutect2.compress_vcfs": "(optional) Boolean?", | ||
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| "##_COMMENT6": "Docker", | ||
| "Mutect2_Panel.gatk_docker": "broadinstitute/gatk:4.1.2.0", | ||
| "#Mutect2_Panel.Mutect2.oncotator_docker": "(optional) String?", | ||
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| "##_COMMENT7": "Disk space", | ||
| "#Mutect2_Panel.Mutect2.emergency_extra_disk": "(optional) Int?", | ||
| "#Mutect2_Panel.CreatePanel.disk_space": "(optional) Int?", | ||
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| "##_COMMENT8": "Preemptibles", | ||
| "#Mutect2_Panel.preemptible_attempts": "(optional) Int?", | ||
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| "##_COMMENT9": "Addtional Runtime Parameters", | ||
| "#Mutect2_Panel.CreatePanel.mem": "(optional) Int?", | ||
| "#Mutect2_Panel.CreatePanel.cpu": "(optional) Int?" | ||
| "##_COMMENT6": "Docker", | ||
| "Mutect2_Panel.gatk_docker":"broadinstitute/gatk:4.1.2.0" | ||
| } |