{ "vip": { "filter_field": { "type": "genotype", "name": "VIPC_S" }, "params": { "assembly": "GRCh38", "GRCh37": { "reference": { "fasta": "/path/to/vip/resources/GRCh37/human_g1k_v37.fasta.gz", "fastaFai": "/path/to/vip/resources/GRCh37/human_g1k_v37.fasta.gz.fai", "fastaGzi": "/path/to/vip/resources/GRCh37/human_g1k_v37.fasta.gz.gzi" }, "chain": { "GRCh38": "/path/to/vip/resources/b37ToHg38.over.chain" } }, "GRCh38": { "reference": { "fasta": "/path/to/vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz", "fastaFai": "/path/to/vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.fai", "fastaGzi": "/path/to/vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.gzi" } }, "T2T": { "reference": { "fasta": "", "fastaFai": "", "fastaGzi": "" }, "chain": { "GRCh38": "/path/to/vip/resources/chm13v2-hg38.over.chain.gz" } }, "cram": { "call_snv": false, "call_str": true, "call_sv": false, "call_cnv": false }, "vcf": { "start": "", "annotate": { "annotsv_cache_dir": "/path/to/vip/resources/annotsv/v3.3.6", "ensembl_gene_mapping": "/path/to/vip/resources/biomart_ensembl_entrez_mapping.txt", "gado_genes": "/path/to/vip/resources/gado/v1.0.4_HPO_v2024-04-04/genesProteinCoding.txt", "gado_hpo": "/path/to/vip/resources/gado/v1.0.4_HPO_v2024-04-04/hp.obo", "gado_predict_info": "/path/to/vip/resources/gado/v1.0.4_HPO_v2024-04-04/HPO_2024_04_04_prediction_info.txt.gz", "gado_predict_matrix": "/path/to/vip/resources/gado/v1.0.4_HPO_v2024-04-04/HPO_2024_04_04_prediction_matrix", "vep_buffer_size": 1000, "vep_cache_dir": "/path/to/vip/resources/vep/cache", "vep_plugin_dir": "/path/to/vip/resources/vep/plugins", "vep_plugin_hpo": "/path/to/vip/resources/hpo_20240404.tsv", "vep_plugin_inheritance": "/path/to/vip/resources/inheritance_20240115.tsv", "vep_plugin_vkgl_mode": 1, "vep_plugin_green_db_enabled": false, "GRCh38": { "capice_model": "/path/to/vip/resources/GRCh38/capice_model_v5.1.2-v3.ubj", "expansionhunter_variant_catalog": "/path/to/vip/resources/GRCh38/expansionhunter_variant_catalog.json", "stranger_catalog": "/path/to/vip/resources/GRCh38/variant_catalog_grch38_fixed.json", "vep_custom_phylop": "/path/to/vip/resources/GRCh38/hg38.phyloP100way.bw", "vep_plugin_clinvar": "/path/to/vip/resources/GRCh38/clinvar_20241001-stripped.tsv.gz", "vep_plugin_gnomad": "/path/to/vip/resources/GRCh38/gnomad.total.v4.1.sites.stripped.tsv.gz", "vep_plugin_spliceai_indel": "/path/to/vip/resources/GRCh38/spliceai_scores.masked.indel.hg38.vcf.gz", "vep_plugin_spliceai_snv": "/path/to/vip/resources/GRCh38/spliceai_scores.masked.snv.hg38.vcf.gz", "vep_plugin_utrannotator": "/path/to/vip/resources/GRCh38/uORF_5UTR_PUBLIC.txt", "vep_plugin_vkgl": "/path/to/vip/resources/GRCh38/vkgl_consensus_20240701.tsv", "vep_plugin_alphscore": "/path/to/vip/resources/GRCh38/AlphScore_final_20230825_stripped_GRCh38.tsv.gz", "vep_plugin_ncer": "/path/to/vip/resources/GRCh38/GRCh38_ncER_perc.bed.gz", "vep_plugin_green_db": "/path/to/vip/resources/GRCh38/GRCh38_GREEN-DB.bed.gz", "vep_plugin_fathmm_MKL_scores": "/path/to/vip/resources/GRCh38/GRCh38_FATHMM-MKL_NC.tsv.gz", "vep_plugin_ReMM_scores": "/path/to/vip/resources/GRCh38/GRCh38_ReMM.tsv.gz" } }, "classify": { "annotate_path": 1, "metadata": "/path/to/vip/resources/field_metadata.json", "GRCh38": { "decision_tree": "/path/to/vip/resources/decision_tree_GRCh38.json" } }, "classify_samples": { "annotate_path": 1, "metadata": "/path/to/vip/resources/field_metadata.json", "GRCh38": { "decision_tree": "/path/to/vip/resources/decision_tree_samples.json" } }, "filter": { "classes": "VUS,LP,P", "consequences": true }, "filter_samples": { "classes": "OK,U1,U2" }, "report": { "include_crams": true, "max_records": "", "max_samples": "", "template": "/path/to/vip/resources/vip-report-template-v6.2.0.html", "metadata": "/path/to/vip/resources/field_metadata.json", "GRCh38": { "genes": "/path/to/vip/resources/GRCh38/GCF_000001405.39_GRCh38.p13_genomic_mapped.gff.gz" } } }, "input": "/path/to/vip/test/suites/vcf/resources/empty_input.tsv", "output": "/path/to/vip/test/output/vcf/empty_input" } }, "sample_variants": { "sorts": { "all": [ { "selected": true, "orders": [ { "direction": "desc", "field": { "type": "info", "name": "CSQ/CAPICE_SC" } } ] }, { "selected": false, "orders": [ { "direction": "asc", "field": { "type": "info", "name": "CSQ/CAPICE_SC" } } ] }, { "selected": false, "orders": [ { "direction": "desc", "field": { "type": "info", "name": "CSQ/gnomAD_HN" } } ] }, { "selected": false, "orders": [ { "direction": "asc", "field": { "type": "info", "name": "CSQ/gnomAD_HN" } } ] } ], "str": [ { "selected": false, "orders": [ { "direction": "desc", "field": { "type": "info", "name": "STR_NORMAL_MAX" } } ] }, { "selected": false, "orders": [ { "direction": "asc", "field": { "type": "info", "name": "STR_NORMAL_MAX" } } ] }, { "selected": false, "orders": [ { "direction": "desc", "field": { "type": "info", "name": "STR_PATHOLOGIC_MIN" } } ] }, { "selected": false, "orders": [ { "direction": "asc", "field": { "type": "info", "name": "STR_PATHOLOGIC_MIN" } } ] } ] }, "cells": { "all": [ { "type": "composed", "name": "locus" }, { "type": "fixed", "name": "ref" }, { "type": "info", "name": "SVTYPE", "label": "Type" }, { "type": "composed", "name": "genotype", "label": "Proband" }, { "type": "composed", "name": "genotype_maternal", "label": "Mother" }, { "type": "composed", "name": "genotype_paternal", "label": "Father" }, { "type": "group", "fields": [ { "type": "info", "name": "CSQ/Consequence" }, { "type": "composed", "name": "gene" }, { "type": "composed", "name": "inheritancePattern" }, { "type": "composed", "name": "hpo" }, { "type": "info", "name": "CSQ/HGVSc" }, { "type": "info", "name": "CSQ/HGVSp" }, { "type": "info", "name": "CSQ/CAPICE_SC" }, { "type": "composed", "name": "vipC" }, { "type": "composed", "name": "vipCS" }, { "type": "composed", "name": "vkgl" }, { "type": "composed", "name": "clinVar" }, { "type": "composed", "name": "gnomAdAf" }, { "type": "info", "name": "CSQ/gnomAD_HN" }, { "type": "info", "name": "CSQ/PUBMED" } ] } ], "snv": [ { "type": "composed", "name": "locus" }, { "type": "fixed", "name": "ref" }, { "type": "info", "name": "SVTYPE" }, { "type": "composed", "name": "genotype", "label": "Proband" }, { "type": "composed", "name": "genotype_maternal", "label": "Mother" }, { "type": "composed", "name": "genotype_paternal", "label": "Father" }, { "type": "group", "fields": [ { "type": "info", "name": "CSQ/Consequence" }, { "type": "composed", "name": "gene" }, { "type": "info", "name": "CSQ/IncompletePenetrance" }, { "type": "composed", "name": "inheritancePattern" }, { "type": "info", "name": "CSQ/HGVSc" }, { "type": "info", "name": "CSQ/HGVSp" }, { "type": "info", "name": "CSQ/CAPICE_SC" }, { "type": "composed", "name": "vipC" }, { "type": "composed", "name": "vipCS" }, { "type": "composed", "name": "vkgl" }, { "type": "info", "name": "CSQ/clinVar_CLNSIG" }, { "type": "info", "name": "CSQ/gnomAD_AF" }, { "type": "info", "name": "CSQ/gnomAD_HN" }, { "type": "info", "name": "CSQ/PUBMED" } ] } ], "str": [ { "type": "composed", "name": "locus" }, { "type": "composed", "name": "genotype", "label": "Proband" }, { "type": "composed", "name": "genotype_maternal", "label": "Mother" }, { "type": "composed", "name": "genotype_paternal", "label": "Father" }, { "type": "composed", "name": "confidenceInterval" }, { "type": "genotype", "name": "LC" }, { "type": "composed", "name": "spanningReads" }, { "type": "info", "name": "STR_NORMAL_MAX" }, { "type": "info", "name": "STR_PATHOLOGIC_MIN" }, { "type": "group", "fields": [ { "type": "composed", "name": "gene" }, { "type": "info", "name": "CSQ/Feature" }, { "type": "composed", "name": "inheritancePattern" }, { "type": "composed", "name": "vipC" }, { "type": "composed", "name": "vipCS" } ] } ] }, "filters": { "all": [ { "type": "composed", "name": "locus" }, { "type": "info", "name": "CSQ/SYMBOL" }, { "type": "info", "name": "CSQ/PICK" }, { "type": "composed", "name": "hpo", "label": "Gene-phenotype association (HPO)" }, { "type": "info", "name": "CSQ/GADO_PD", "label": "Gene-phenotype association (GADO)" }, { "type": "info", "name": "CSQ/IncompletePenetrance" }, { "type": "composed", "name": "vipC" }, { "type": "composed", "name": "vipCS" }, { "type": "info", "name": "CSQ/VKGL_CL" }, { "type": "info", "name": "CSQ/clinVar_CLNSIG" }, { "type": "genotype", "name": "VI" }, { "type": "composed", "name": "inheritanceMatch", "label": "Inheritance match", "description": "Indication if the inheritance pattern of any gene associated with the variant matches the inheritance pattern suitable for the samples in the family of the sample. For more information see https://github.com/molgenis/vip-inheritance-matcher ." }, { "type": "composed", "name": "deNovo", "label": "De Novo", "description": "Indication if the variant is De Novo or inherited from the parents of the sample." }, { "type": "composed", "name": "allelicImbalance", "label": "Allelic Imbalance", "description": "Sample genotype shows allelic imbalance, calculated by: the allelic depth (AD) value of the first allele divided by the sum of the AD values for the genotype. For hetrozygotic genotypes values below 0.02 or above 0.8 are considered imbalanced. For homozygotic genotypes values between 0.02 and 0.98 are considered imbalanced." } ], "str": [ { "type": "composed", "name": "locus" }, { "type": "info", "name": "CSQ/PICK", "defaultValue": "true" }, { "type": "info", "name": "CSQ/HPO", "label": "Gene-phenotype association (HPO)" }, { "type": "info", "name": "CSQ/GADO_PD", "label": "Gene-phenotype association (GADO)" }, { "type": "info", "name": "CSQ/SYMBOL" }, { "type": "composed", "name": "vipC" }, { "type": "composed", "name": "vipCS" } ] }, "recordsPerPage": { "str": [ { "number": 10 }, { "number": 20, "selected": true }, { "number": 50 }, { "number": 100 } ] } }, "variants": { "cells": { "all": [ { "type": "composed", "name": "locus" }, { "type": "fixed", "name": "id" }, { "type": "fixed", "name": "ref" }, { "type": "fixed", "name": "alt" }, { "type": "fixed", "name": "qual" }, { "type": "fixed", "name": "filter" }, { "type": "info", "name": ".*" } ] }, "filters": { "all": [ { "type": "composed", "name": "locus" }, { "type": "fixed", "name": "id" }, { "type": "fixed", "name": "ref" }, { "type": "fixed", "name": "alt" }, { "type": "fixed", "name": "qual" }, { "type": "fixed", "name": "filter" }, { "type": "info", "name": ".*" } ] } }, "sample_variant": { "cells": { "all": [ { "type": "composed", "name": "vipC" }, { "type": "composed", "name": "vipCS" }, { "type": "info", "name": "CSQ/((?!VIPC|VIPP).)*" } ] }, "sample_cells": { "all": [ { "type": "composed", "name": "genotype", "label": "Genotype" }, { "type": "genotype", "name": "((?!GT|VIPC_S|VIPP_S).)*" } ] } }, "variant": { "cells": { "all": [ { "type": "composed", "name": "vipC" }, { "type": "info", "name": "CSQ/((?!VIPC|VIPP).)*" } ] } }, "sample_variant_consequence": { "sample_cells": { "all": [ { "type": "composed", "name": "genotype", "label": "Genotype" }, { "type": "genotype", "name": "((?!GT|VIPC_S|VIPP_S).)*" } ] } }, "variant_consequence": {} }