dias_TWE_config_GRCh37_v3.0.1.json

{
    "assay": "TWE",
    "version": "3.0.1",
    "snv_report_workflow_id": "workflow-GXzkfYj4QPQp9z4Jz4BF09y6",
    "reference_files": {
        "genepanels": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GVx0vkQ433Gvq63k1Kj4Y562",
        "exons_nirvana": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF611Z8433Gk7gZ47gypK7ZZ",
        "genes2transcripts": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GV4P970433Gj6812zGVBZvB4",
        "exonsfile": "project-Fkb6Gkj433GVVvj73J7x8KbV:file-GF611Z8433Gf99pBPbJkV7bq"
    },
    "name_patterns": {
        "Epic": "^[\\d\\w]+-[\\d\\w]+",
        "Gemini": "^X[\\d]+"
    },
    "modes": {
        "snv_reports": {
            "stage_instance_types": {
            },
            "inputs": {
                "stage-rpt_generate_bed_athena.exons_nirvana": "INPUT-exons_nirvana",
                "stage-rpt_generate_bed_athena.nirvana_genes2transcripts": "INPUT-genes2transcripts",
                "stage-rpt_generate_bed_athena.gene_panels": "INPUT-genepanels",
                "stage-rpt_generate_bed_vep.exons_nirvana": "INPUT-exons_nirvana",
                "stage-rpt_generate_bed_vep.nirvana_genes2transcripts": "INPUT-genes2transcripts",
                "stage-rpt_generate_bed_vep.gene_panels": "INPUT-genepanels",
                "stage-rpt_generate_bed_vep.flank": 495,
                "stage-rpt_vep.config_file": {
                    "$dnanexus_link": {
                        "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
                        "id": "file-Gf0q8fj4j4fZG84VJ9YYvKVk"
                    }
                },
                "stage-rpt_vep.vcf": {
                    "folder": "sentieon-dnaseq",
                    "name": "^[^\\.]*(?!\\.g)\\.vcf(\\.gz)?$"
                },
                "stage-rpt_vep.buffer_size": 1000,
                "stage-rpt_generate_workbook.exclude_columns": "BaseQRankSum ClippingRankSum DB ExcessHet FS MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR PL QUAL ID FILTER  CSQ_ClinVar_CLNSIGCONF  CSQ_Allele CSQ_HGNC_ID DP AC AF AN CSQ_SpliceAI_pred_DP_AL CSQ_SpliceAI_pred_DP_AG CSQ_SpliceAI_pred_DP_DG CSQ_SpliceAI_pred_DP_DL CSQ_gnomADe_AC_popmax CSQ_gnomADe_AF_popmax CSQ_gnomADe_AN_popmax CSQ_gnomADe_nhomalt_popmax CSQ_gnomADe_non_cancer_AC CSQ_gnomADe_non_cancer_AC_popmax CSQ_gnomADe_non_cancer_AF CSQ_gnomADe_non_cancer_AF_popmax CSQ_gnomADe_non_cancer_AN CSQ_gnomADe_non_cancer_AN_popmax CSQ_gnomADe_non_cancer_nhomalt CSQ_gnomADe_non_cancer_nhomalt_popmax CSQ_gnomADe_non_cancer_popmax CSQ_gnomADe_popmax CSQ_gnomADg_AC_popmax CSQ_gnomADg_AF_popmax CSQ_gnomADg_AN_popmax CSQ_gnomADg_nhomalt_popmax CSQ_gnomADg_popmax",
                "stage-rpt_generate_workbook.acmg": true,
                "stage-rpt_generate_workbook.rename_columns": "CSQ_Feature=Transcript DP_FMT=DP",
                "stage-rpt_generate_workbook.add_comment_column": true,
                "stage-rpt_generate_workbook.keep_tmp": true,
                "stage-rpt_generate_workbook.summary": "dias",
                "stage-rpt_generate_workbook.filter": "bcftools filter -e '(CSQ_Consequence==\"synonymous_variant\" | CSQ_Consequence==\"intron_variant\" | CSQ_Consequence==\"upstream_gene_variant\" | CSQ_Consequence==\"downstream_gene_variant\" | CSQ_Consequence==\"intergenic_variant\" | CSQ_Consequence==\"5_prime_UTR_variant\" | CSQ_Consequence==\"3_prime_UTR_variant\" | CSQ_gnomADe_AF>0.01 | CSQ_gnomADg_AF>0.01 | CSQ_TWE_AF>0.05) & CSQ_HGMD_CLASS!~ \"DM\" & CSQ_ClinVar_CLNSIG!~ \"pathogenic\\/i\" & CSQ_ClinVar_CLNSIGCONF!~ \"pathogenic\\/i\"'",
                "stage-rpt_generate_workbook.human_filter": "excluded gnomAD exomes / genomes > 1%, TWE > 5%, synonymous / intronic / intergenic / upstream / downstream / UTRs EXCEPT pathogenic status in ClinVar OR DM in HGMD Class",
                "stage-rpt_generate_workbook.reorder_columns": "CHROM POS REF ALT GT GQ DP_FMT AD CSQ_SYMBOL CSQ_EXON CSQ_INTRON CSQ_HGVSc CSQ_HGVSp CSQ_Consequence CSQ_IMPACT CSQ_VARIANT_CLASS CSQ_gnomADe_AF CSQ_gnomADe_Hom CSQ_gnomADe_AC CSQ_gnomADe_AN CSQ_gnomADe_nhomalt CSQ_gnomADg_AF CSQ_gnomADg_AC CSQ_gnomADg_AN CSQ_gnomADg_nhomalt CSQ_TWE_AF CSQ_TWE_AC_Hom CSQ_TWE_AC_Het CSQ_TWE_AN CSQ_HGMD CSQ_HGMD_CLASS CSQ_HGMD_RANKSCORE CSQ_HGMD_PHEN CSQ_Existing_variation CSQ_ClinVar CSQ_ClinVar_CLNDN CSQ_ClinVar_CLNSIG CSQ_Mastermind_MMID3 CSQ_CADD_PHRED CSQ_REVEL CSQ_SpliceAI_pred_DS_AG CSQ_SpliceAI_pred_DS_AL CSQ_SpliceAI_pred_DS_DG CSQ_SpliceAI_pred_DS_DL CSQ_HGVS_OFFSET CSQ_STRAND CSQ_Feature",
                "stage-rpt_generate_workbook.freeze_column": "N2",
                "stage-rpt_athena.exons_file": "INPUT-exonsfile",
                "stage-rpt_athena.limit": 260,
                "stage-rpt_athena.summary": true,
                "stage-rpt_athena.mosdepth_files": {
                    "folder": "eggd_mosdepth",
                    "name": "per-base.bed.gz$|reference_build.txt$"
                }
            }
        }
    }
}