GPF Study Configuration ======================= * ``id`` - ID of the study. This is a required field. * ``name`` - display name of the study. If the ``name`` is not specified, the ``id`` will be used as the display name. * ``enabled`` - whether the study is enabled. * ``description_file`` - path to the study description file. * ``study_phenotype`` - study phenotype. * ``has_denovo`` - whether the study has de novo variants. * ``has_transmitted`` - whether the study has transmitted variants. * ``has_cnv`` - whether the study has CNV variants. * ``has_complex`` - whether the study has complex variants. * ``has_tandem_repeat`` - whether the study has tandem repeat variants. * ``has_zygosity`` - whether the study has zygosity information. * ``phenotype_data`` - phenotype data associated with the study. * ``phenotype_browser`` - whether the phenotype browser is enabled. * ``phenotype_tool`` - whether the phenotype tool is enabled. * ``person_set_collections`` - section to define person set collections associated with the study. * ``genotype_storage`` - section to define genotype storage configuration for the study. * ``genotype browser`` - section to define genotype browser configuration for the study. * ``common_report`` - section to define common report configuration for the study. * ``denovo_gene_sets`` - section to define de novo gene sets configuration for the study. * ``enrichment`` - section to define enrichment configuration for the study. * ``gene_browser`` - section to define gene browser configuration for the study. .. code-block:: yaml :linenos: id: example_study phenotype_browser: false phenotype_tool: false study_type: - WE study_phenotype: autism has_transmitted: false has_denovo: true has_complex: false has_cnv: false person_set_collections: selected_person_set_collections: - phenotype phenotype: id: phenotype name: Phenotype sources: - from: pedigree source: status domain: - id: autism name: autism values: - affected color: '#ff2121' - id: unaffected name: unaffected values: - unaffected color: '#ffffff' default: id: unspecified name: unspecified color: '#aaaaaa' genotype_browser: enabled: true has_present_in_child: true has_present_in_parent: true has_pedigree_selector: true variant_types: - sub - ins - del - complex columns: genotype: pedigree: name: pedigree source: pedigree worst_effect: name: worst effect source: worst_effect genes: name: genes source: genes lgd_rank: name: LGD rank source: LGD_rank format: '%%d' rvis_rank: name: RVIS rank source: RVIS_rank format: '%%d' pli_rank: name: pLI rank source: pLI_rank format: '%%d' family_id: name: family id source: family study: name: study source: study_name family_person_ids: name: family person ids source: family_person_ids location: name: location source: location variant: name: variant source: variant chrom: name: CHROM source: chrom position: name: POS source: position reference: name: REF source: reference alternative: name: ALT source: alternative carrier_person_ids: name: carrier person ids source: carrier_person_ids carrier_person_attributes: name: carrier person attributes source: carrier_person_attributes family_person_attributes: name: family person attributes source: family_person_attributes family_phenotypes: name: family phenotypes source: family_phenotypes carrier_phenotypes: name: carrier phenotypes source: carrier_phenotypes inheritance: name: inheritance type source: inheritance_type study_phenotype: name: study phenotype source: study_phenotype best: name: family best state source: best_st family_genotype: name: family genotype source: genotype family_structure: name: family structure source: family_structure geneeffect: name: all effects source: effects effectdetails: name: effect details source: effect_details alt_alleles: name: alt alleles source: af_allele_count par_called: name: parents called source: af_parents_called_count allele_freq: name: allele frequency source: af_allele_freq seen_as_denovo: name: seen_as_denovo source: seen_as_denovo seen_in_affected: name: seen_in_affected source: seen_in_affected seen_in_unaffected: name: seen_in_unaffected source: seen_in_unaffected phylop_phylop100way: name: 100way source: phylop100way format: '%%.3f' phylop_phylop30way: name: 30way source: phylop30way format: '%%.3f' phylop_phylop20way: name: 20way source: phylop20way format: '%%.3f' phastcons_phastcons100way: name: 100way source: phastcons100way format: '%%.3f' phastcons_phastcons30way: name: 30way source: phastcons30way format: '%%.3f' phastcons_phastcons20way: name: 20way source: phastcons20way format: '%%.3f' fitcons_fitcons2_e073: name: Prefrontal Cortex source: fitcons2_e073 format: '%%.3f' fitcons_fitcons2_e081: name: ' Male Fetal' source: fitcons2_e081 format: '%%.3f' fitcons_fitcons2_e082: name: Female Fetal source: fitcons2_e082 format: '%%.3f' freq_ssc: name: SSC source: ssc_freq format: '%%.3f' freq_exome_gnomad: name: exome gnomAD source: exome_gnomad_v2_1_1_af_percent format: '%%.3f' freq_genome_gnomad: name: genome gnomAD source: genome_gnomad_v3_af_percent format: '%%.3f' cadd_raw: name: CADD raw source: cadd_raw format: '%%.3f' cadd_phred: name: CADD phred source: cadd_phred format: '%%.3f' mpc: name: MPC source: mpc format: '%%.3f' linsight: name: Linsight source: linsight format: '%%.3f' genome_gnomad_v2_1_1_ac: name: genome_gnomad_v2_1_1_ac source: genome_gnomad_v2_1_1_ac format: '%%d' genome_gnomad_v2_1_1_an: name: genome_gnomad_v2_1_1_an source: genome_gnomad_v2_1_1_an format: '%%d' genome_gnomad_v2_1_1_controls_ac: name: genome_gnomad_v2_1_1_controls_ac source: genome_gnomad_v2_1_1_controls_ac format: '%%d' genome_gnomad_v2_1_1_controls_an: name: genome_gnomad_v2_1_1_controls_an source: genome_gnomad_v2_1_1_controls_an format: '%%d' genome_gnomad_v2_1_1_non_neuro_ac: name: genome_gnomad_v2_1_1_non_neuro_ac source: genome_gnomad_v2_1_1_non_neuro_ac format: '%%d' genome_gnomad_v2_1_1_non_neuro_an: name: genome_gnomad_v2_1_1_non_neuro_an source: genome_gnomad_v2_1_1_non_neuro_an format: '%%d' genome_gnomad_v2_1_1_af_percent: name: genome_gnomad_v2_1_1_af_percent source: genome_gnomad_v2_1_1_af_percent format: '%%.3f' genome_gnomad_v2_1_1_controls_af_percent: name: genome_gnomad_v2_1_1_controls_af_percent source: genome_gnomad_v2_1_1_controls_af_percent format: '%%.3f' genome_gnomad_v2_1_1_non_neuro_af_percent: name: genome_gnomad_v2_1_1_non_neuro_af_percent source: genome_gnomad_v2_1_1_non_neuro_af_percent format: '%%.3f' exome_gnomad_v2_1_1_ac: name: exome_gnomad_v2_1_1_ac source: exome_gnomad_v2_1_1_ac format: '%%d' exome_gnomad_v2_1_1_an: name: exome_gnomad_v2_1_1_an source: exome_gnomad_v2_1_1_an exome_gnomad_v2_1_1_controls_ac: name: exome_gnomad_v2_1_1_controls_ac source: exome_gnomad_v2_1_1_controls_ac format: '%%d' exome_gnomad_v2_1_1_controls_an: name: exome_gnomad_v2_1_1_controls_an source: exome_gnomad_v2_1_1_controls_an format: '%%d' exome_gnomad_v2_1_1_non_neuro_ac: name: exome_gnomad_v2_1_1_non_neuro_ac source: exome_gnomad_v2_1_1_non_neuro_ac format: '%%d' exome_gnomad_v2_1_1_non_neuro_an: name: exome_gnomad_v2_1_1_non_neuro_an source: exome_gnomad_v2_1_1_non_neuro_an format: '%%d' exome_gnomad_v2_1_1_af_percent: name: exome_gnomad_v2_1_1_af_percent source: exome_gnomad_v2_1_1_af_percent format: '%%.3f' exome_gnomad_v2_1_1_controls_af_percent: name: exome_gnomad_v2_1_1_controls_af_percent source: exome_gnomad_v2_1_1_controls_af_percent format: '%%.3f' exome_gnomad_v2_1_1_non_neuro_af_percent: name: exome_gnomad_v2_1_1_non_neuro_af_percent source: exome_gnomad_v2_1_1_non_neuro_af_percent format: '%%.3f' genome_gnomad_v3_ac: name: genome_gnomad_v3_ac source: genome_gnomad_v3_ac format: '%%d' genome_gnomad_v3_an: name: genome_gnomad_v3_an source: genome_gnomad_v3_an format: '%%d' genome_gnomad_v3_af_percent: name: genome_gnomad_v3_af_percent source: genome_gnomad_v3_af_percent format: '%%.3f' phylop100way: name: phyloP100way source: phylop100way format: '%%.3f' phylop30way: name: phyloP30way source: phylop30way format: '%%.3f' phylop20way: name: phyloP20way source: phylop20way format: '%%.3f' phylop7way: name: phyloP7way source: phylop7way format: '%%.3f' phastcons100way: name: phastCons100way source: phastcons100way format: '%%.3f' phastcons30way: name: phastCons30way source: phastcons30way format: '%%.3f' phastcons20way: name: phastCons20way source: phastcons20way format: '%%.3f' phastcons7way: name: phastCons7way source: phastcons7way format: '%%.3f' fitcons_i6_merged: name: FitCons i6 merged source: fitcons_i6_merged format: '%%.3f' fitcons2_e067: name: FitCons2 Brain Angular Gyrus source: fitcons2_e067 format: '%%.3f' fitcons2_e068: name: FitCons2 Brain Anterior Caudate source: fitcons2_e068 format: '%%.3f' fitcons2_e069: name: FitCons2 Brain Cingulate Gyrus source: fitcons2_e069 format: '%%.3f' fitcons2_e070: name: FitCons2 Brain Germinal Matrix source: fitcons2_e070 format: '%%.3f' fitcons2_e071: name: FitCons2 Brain Hippocampus Middle source: fitcons2_e071 format: '%%.3f' fitcons2_e072: name: FitCons2 Brain Inferior Temporal Lobe source: fitcons2_e072 format: '%%.3f' fitcons2_e073: name: FitCons2 Brain Dorsolateral Prefrontal Cortex source: fitcons2_e073 format: '%%.3f' fitcons2_e074: name: FitCons2 Brain Substantia Nigra source: fitcons2_e074 format: '%%.3f' fitcons2_e081: name: FitCons2 Fetal Brain Male source: fitcons2_e081 format: '%%.3f' fitcons2_e082: name: FitCons2 Fetal Brain Female source: fitcons2_e082 format: '%%.3f' column_groups: genotype: name: genotype columns: - pedigree - carrier_person_attributes - family_person_attributes effect: name: effect columns: - worst_effect - genes gene_scores: name: vulnerability/intolerance columns: - lgd_rank - rvis_rank - pli_rank family: name: family columns: - family_id - study variant: name: variant columns: - location - variant variant_extra: name: variant columns: - chrom - position - reference - alternative carriers: name: carriers columns: - carrier_person_ids - carrier_person_attributes phenotypes: name: phenotypes columns: - family_phenotypes - carrier_phenotypes mpc_cadd: name: MPC and CADD columns: - mpc - cadd_raw - cadd_phred phylop: name: phyloP columns: - phylop_phylop100way - phylop_phylop30way - phylop_phylop20way phastcons: name: phastCons columns: - phastcons_phastcons100way - phastcons_phastcons30way - phastcons_phastcons20way fitcons: name: FitCons Brain columns: - fitcons_fitcons2_e073 - fitcons_fitcons2_e081 - fitcons_fitcons2_e082 freq: name: Frequency columns: - freq_ssc - freq_exome_gnomad - freq_genome_gnomad preview_columns: - family - variant - genotype - effect - gene_scores - phylop - phastcons - mpc_cadd - fitcons - freq download_columns: - family - study_phenotype - variant - variant_extra - family_person_ids - family_structure - best - family_genotype - carriers - inheritance - phenotypes - par_called - allele_freq - effect - geneeffect - effectdetails - gene_scores - phylop100way - phylop30way - phylop20way - phylop7way - phastcons100way - phastcons30way - phastcons20way - phastcons7way - cadd_raw - cadd_phred - mpc - linsight - fitcons_i6_merged - fitcons2_e067 - fitcons2_e068 - fitcons2_e069 - fitcons2_e070 - fitcons2_e071 - fitcons2_e072 - fitcons2_e073 - fitcons2_e074 - fitcons2_e081 - fitcons2_e082 - genome_gnomad_v2_1_1_ac - genome_gnomad_v2_1_1_an - genome_gnomad_v2_1_1_controls_ac - genome_gnomad_v2_1_1_controls_an - genome_gnomad_v2_1_1_non_neuro_ac - genome_gnomad_v2_1_1_non_neuro_an - genome_gnomad_v2_1_1_af_percent - genome_gnomad_v2_1_1_controls_af_percent - genome_gnomad_v2_1_1_non_neuro_af_percent - exome_gnomad_v2_1_1_ac - exome_gnomad_v2_1_1_an - exome_gnomad_v2_1_1_controls_ac - exome_gnomad_v2_1_1_controls_an - exome_gnomad_v2_1_1_non_neuro_ac - exome_gnomad_v2_1_1_non_neuro_an - exome_gnomad_v2_1_1_af_percent - exome_gnomad_v2_1_1_controls_af_percent - exome_gnomad_v2_1_1_non_neuro_af_percent - genome_gnomad_v3_ac - genome_gnomad_v3_an - genome_gnomad_v3_af_percent common_report: enabled: true effect_groups: - LGDs - nonsynonymous - UTRs - CNV effect_types: - Nonsense - Frame-shift - Splice-site - Missense - No-frame-shift - noStart - noEnd - Synonymous - Non coding - Intron - Intergenic - 3'-UTR - 5'-UTR denovo_gene_sets: enabled: true selected_person_set_collections: - phenotype standard_criterias: effect_types: segments: LGDs: LGDs Missense: missense Synonymous: synonymous sexes: segments: Female: F Male: M Unspecified: U recurrency_criteria: segments: Single: start: 1 end: 2 Triple: start: 3 end: -1 Recurrent: start: 2 end: -1 gene_sets_names: - LGDs - LGDs.Male - LGDs.Female - LGDs.Recurrent - LGDs.Triple - Missense - Missense.Male - Missense.Female - Missense.Recurrent - Missense.Triple - Synonymous - Synonymous.Male - Synonymous.Female - Synonymous.Recurrent - Synonymous.Triple enrichment: enabled: false selected_person_set_collections: - phenotype selected_background_models: - hg38/enrichment/coding_length_ref_gene_v20170601 - enrichment/samocha_background - hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_2 - hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_CSHL - hg38/enrichment/ur_synonymous_w1202s766e611_liftover - hg38/enrichment/ur_synonymous_iWES_v1_1 - hg38/enrichment/ur_synonymous_iWES_v2 - hg38/enrichment/ur_synonymous_iWGS_v1_1 - hg38/enrichment/ur_synonymous_AGRE_WG38_859 default_background_model: enrichment/samocha_background selected_counting_models: - enrichment_events_counting - enrichment_gene_counting counting: enrichment_events_counting: id: enrichment_events_counting name: Counting events desc: Counting events enrichment_gene_counting: id: enrichment_gene_counting name: Counting affected genes desc: Counting affected genes default_counting_model: enrichment_events_counting effect_types: - LGDs - missense - synonymous gene_browser: enabled: true frequency_column: genome_gnomad_v3_af_percent frequency_name: genome GnomAD %% effect_column: effect.worst effect type location_column: variant.location domain_min: 0.01 domain_max: 100