Packages

package raw

Type Members

  1. case class GENOTYPES(sampleId: Option[String] = Some("id")) extends Product with Serializable
  2. case class InfoCSQ(Allele: String = "C", Consequence: List[String] = List("synonymous_variant"), IMPACT: String = "LOW", SYMBOL: String = "OR4F5", Gene: String = "ENSG00000186092", Feature_type: String = "Transcript", Feature: String = "ENST00000335137", BIOTYPE: String = "protein_coding", EXON: Exon = Exon("1", 1), INTRON: Intron = Intron(None, None), HGVSc: String = "ENST00000335137.4:c.807T>C", HGVSp: String = "ENSP00000334393.3:p.Ser269%3D", cDNA_position: Int = 843, CDS_position: Int = 807, Protein_position: Int = 269, Amino_acids: AminoAcids = AminoAcids("S", None), Codons: CODONS = CODONS("tcT", "tcC"), Existing_variation: List[String] = List("rs200676709"), DISTANCE: Option[Int] = None, STRAND: Int = 1, FLAGS: Option[List[String]] = None, PICK: String = "1", VARIANT_CLASS: String = "SNV", SYMBOL_SOURCE: String = "HGNC", HGNC_ID: String = "HGNC:14825", CANONICAL: String = "YES", RefSeq: String = ..., HGVS_OFFSET: Option[String] = None, HGVSg: String = "chr1:g.69897T>C", CLIN_SIG: Option[String] = None, SOMATIC: Option[String] = None, PHENO: Option[String] = None, PUBMED: Option[String] = Some("29135816"), CADD_raw_rankscore: Option[String] = None, DANN_rankscore: Option[String] = None, Ensembl_geneid: Option[String] = None, Ensembl_transcriptid: Option[String] = None, ExAC_AC: Option[String] = None, ExAC_AF: Option[String] = None, FATHMM_converted_rankscore: Option[String] = None, FATHMM_pred: Option[String] = None, GTEx_V7_tissue: Option[String] = None, Interpro_domain: Option[String] = None, LRT_converted_rankscore: Option[String] = None, LRT_pred: Option[String] = None, Polyphen2_HVAR_pred: Option[String] = None, Polyphen2_HVAR_rankscore: Option[String] = None, REVEL_rankscore: Option[String] = None, SIFT_converted_rankscore: Option[String] = None, SIFT_pred: Option[String] = None, UK10K_AC: Option[String] = None, UK10K_AF: Option[String] = None, clinvar_MedGen_id: Option[String] = None, clinvar_OMIM_id: Option[String] = None, clinvar_Orphanet_id: Option[String] = None, clinvar_clnsig: Option[String] = None, clinvar_id: Option[String] = None, clinvar_trait: Option[String] = None, gnomAD_exomes_AC: Option[String] = None, gnomAD_exomes_AF: Option[String] = None, gnomAD_genomes_AC: Option[String] = None, gnomAD_genomes_AF: Option[String] = None, phyloP17way_primate_rankscore: Option[String] = None, rs_dbSNP151: Option[String] = None) extends Product with Serializable
  3. case class RawAnnovarScores(#Chr: String = "1", Start: String = "69091", End: String = "69091", Ref: String = "A", Alt: String = "C", DamagePredCount: String = "1.17", SIFT_pred: String = "T", SIFT4G_pred: String = "T", Polyphen2_HDIV_pred: String = "B", Polyphen2_HVAR_pred: String = "B", LRT_pred: String = "N", MutationTaster_pred: Option[String] = None, MutationAssessor_pred: Option[String] = None, FATHMM_pred: String = "T", PROVEAN_pred: String = "N", VEST4_score: String = "0.198", MetaSVM_pred: String = "T", MetaLR_pred: String = "T", M-CAP_pred: String = "T", REVEL_score: String = "0.109", MutPred_score: String = "0.823", MVP_score: Option[String] = None, MPC_score: Option[String] = None, PrimateAI_pred: Option[String] = None, DEOGEN2_pred: String = "T", BayesDel_addAF_pred: String = "T", BayesDel_noAF_pred: String = "T", ClinPred_pred: String = "T", LIST-S2_pred: String = "D", CADD_raw: String = "-0.145", CADD_phred: String = "0.670", DANN_score: String = "0.444", fathmm-MKL_coding_pred: String = "N", fathmm-XF_coding_pred: String = "N", Eigen-raw_coding: String = "-1.394", Eigen-phred_coding: String = "0.119", Eigen-PC-raw_coding: String = "-1.536", Eigen-PC-phred_coding: String = "0.095", GenoCanyon_score: String = "0.000", integrated_fitCons_score: String = "0.487", GM12878_fitCons_score: String = "0.574", H1-hESC_fitCons_score: String = "0.574", HUVEC_fitCons_score: String = "0.564", LINSIGHT: Option[String] = None, GERP++_NR: String = "2.310", GERP++_RS: String = "-4.630", phyloP100way_vertebrate: String = "-0.055", phyloP30way_mammalian: String = "-0.214", phyloP17way_primate: String = "-2.209", phastCons100way_vertebrate: String = "0.000", phastCons30way_mammalian: String = "0.105", phastCons17way_primate: String = "0.000", bStatistic: String = "994", Interpro_domain: Option[String] = None, GTEx_V8_gene: Option[String] = None, GTEx_V8_tissue: Option[String] = None) extends Product with Serializable
  4. case class RawClinvar(contigName: String = "2", start: Long = 69359260, end: Long = 69359261, names: List[String] = List("257668"), referenceAllele: String = "T", alternateAlleles: List[String] = List("A"), qual: Option[Double] = None, filters: List[String] = List(""), splitFromMultiAllelic: Boolean = false, INFO_AF_EXAC: Double = 0.00394, INFO_CLNVCSO: String = "SO:0001483", INFO_GENEINFO: String = "GFPT1:2673", INFO_CLNSIGINCL: Option[List[String]] = None, INFO_CLNVI: List[String] = ..., INFO_CLNDISDB: List[String] = ..., INFO_CLNREVSTAT: List[String] = ..., INFO_CLNDN: List[String] = ..., INFO_ALLELEID: Int = 250763, INFO_ORIGIN: List[String] = List("1"), INFO_SSR: Option[Int] = None, INFO_CLNDNINCL: Option[List[String]] = None, INFO_CLNSIG: List[String] = List("Benign"), INFO_RS: List[String] = List("112682152"), INFO_DBVARID: Option[List[String]] = None, INFO_AF_TGP: Double = 0.01118, INFO_CLNVC: String = "single_nucleotide_variant", INFO_CLNHGVS: List[String] = List("NC_000002.12:g.69359261T>A"), INFO_MC: List[String] = List("SO:0001627|intron_variant"), INFO_CLNSIGCONF: Option[List[String]] = None, INFO_AF_ESP: Double = 0.01415, INFO_CLNDISDBINCL: Option[List[String]] = None, genotypes: List[GENOTYPES] = List(GENOTYPES())) extends Product with Serializable
  5. case class RawCosmicGeneSet(GENE_SYMBOL: String = "RET", NAME: String = "ret proto-oncogene", COSMIC_GENE_ID: String = "COSG68325", CHROMOSOME: String = "10", GENOME_START: String = "43077027", GENOME_STOP: String = "43130351", CHR_BAND: String = "11.21", SOMATIC: String = "y", GERMLINE: String = "y", TUMOUR_TYPES_SOMATIC: String = ..., TUMOUR_TYPES_GERMLINE: String = ..., CANCER_SYNDROME: String = ..., TISSUE_TYPE: String = "E, O", MOLECULAR_GENETICS: String = "Dom", ROLE_IN_CANCER: String = "oncogene, fusion", MUTATION_TYPES: String = "T, Mis, N, F", TRANSLOCATION_PARTNER: String = ..., OTHER_GERMLINE_MUT: String = "y", OTHER_SYNDROME: String = "Hirschsprung disease", TIER: String = "1", SYNONYMS: String = ...) extends Product with Serializable
  6. case class RawCosmicMutationSet(GENE_NAME: String = "SF3B1", ACCESSION_NUMBER: String = "ENST00000335508.6", ONC_TSG: String = "oncogene", CGC_TIER: String = "1", MUTATION_URL: String = ..., LEGACY_MUTATION_ID: String = "COSM84677", Mutation CDS: String = "c.2098A>G", Mutation AA: String = "p.K700E", AA_MUT_START: String = "700", AA_MUT_STOP: String = "700", SHARED_AA: String = "9", GENOMIC_WT_ALLELE_SEQ: String = "T", GENOMIC_MUT_ALLELE_SEQ: String = "C", AA_WT_ALLELE_SEQ: String = "K", AA_MUT_ALLELE_SEQ: String = "E", Mutation Description CDS: String = "Substitution", Mutation Description AA: String = "Substitution - Missense", ONTOLOGY_MUTATION_CODE: String = "SO:0001583", GENOMIC_MUTATION_ID: String = "COSV59205318", Mutation genome position GRCh37: String = "2:198266834-198266834", Mutation genome position GRCh38: String = "2:197402110-197402110", COSMIC_SAMPLE_TESTED: String = "86821", COSMIC_SAMPLE_MUTATED: String = "699", DISEASE: String = ..., WGS_DISEASE: String = ..., EXAC_AF: String = "0.0002", EXAC_AFR_AF: String = "0.0003", EXAC_AMR_AF: String = "8.69e-05", EXAC_ADJ_AF: String = "0.0002", EXAC_EAS_AF: String = "0.0003", EXAC_FIN_AF: String = "0", EXAC_NFE_AF: String = "0.0003", EXAC_SAS_AF: String = "0", GNOMAD_EXOMES_AF: String = "8.97e-05", GNOMAD_EXOMES_AFR_AF: String = "6.21e-05", GNOMAD_EXOMES_AMR_AF: String = "3.11e-05", GNOMAD_EXOMES_ASJ_AF: String = "0.0003", GNOMAD_EXOMES_EAS_AF: String = "0", GNOMAD_EXOMES_FIN_AF: String = "4.64e-05", GNOMAD_EXOMES_NFE_AF: String = "0.0001", GNOMAD_EXOMES_SAS_AF: String = "6.76e-05", GNOMAD_GENOMES_AF: String = "3.94e-05", GNOMAD_GENOMES_AFR_AF: String = "0", GNOMAD_GENOMES_AMI_AF: String = "0", GNOMAD_GENOMES_AMR_AF: String = "0", GNOMAD_GENOMES_ASJ_AF: String = "0", GNOMAD_GENOMES_EAS_AF: String = "0", GNOMAD_GENOMES_FIN_AF: String = "0", GNOMAD_GENOMES_MID_AF: String = "0", GNOMAD_GENOMES_NFE_AF: String = "8.82e-05", GNOMAD_GENOMES_SAS_AF: String = "0", CLINVAR_CLNSIG: String = ..., CLINVAR_TRAIT: String = ..., GERP++_RS: String = "6.02", MIN_SIFT_SCORE: String = "0.004", MIN_SIFT_PRED: String = "D", DNDS_DISEASE_QVAL_SIG: String = "breast=4.73e-24", MUTATION_SIGNIFICANCE_TIER: String = "2") extends Product with Serializable
  7. case class RawGnomadConstraint(gene: String = "ZC3H4", transcript: String = "ENST00000253048", obs_mis: String = "746", exp_mis: String = "7.9816e+02", oe_mis: String = "9.3465e-01", mu_mis: String = "5.4158e-05", possible_mis: String = "8378", obs_mis_pphen: String = "95", exp_mis_pphen: String = "1.1573e+02", oe_mis_pphen: String = "8.2090e-01", possible_mis_pphen: String = "1145", obs_syn: String = "446", exp_syn: String = "3.4301e+02", oe_syn: String = "1.3002e+00", mu_syn: String = "2.5301e-05", possible_syn: String = "2661", obs_lof: String = "0", mu_lof: String = "3.7692e-06", possible_lof: String = "543", exp_lof: String = "5.4645e+01", pLI: String = "1.0000e+00", pNull: String = "1.8815e-22", pRec: String = "2.3777e-09", oe_lof: String = "0.0000e+00", oe_syn_lower: String = "1.2020e+00", oe_syn_upper: String = "1.4060e+00", oe_mis_lower: String = "8.7900e-01", oe_mis_upper: String = "9.9300e-01", oe_lof_lower: String = "0.0000e+00", oe_lof_upper: String = "5.4000e-02", constraint_flag: String = "syn_outlier", syn_z: String = "-4.3711e+00", mis_z: String = "6.5604e-01", lof_z: String = "6.8501e+00", oe_lof_upper_rank: String = "22", oe_lof_upper_bin: String = "0", oe_lof_upper_bin_6: String = "0", n_sites: String = "10", classic_caf: String = "4.7040e-05", max_af: String = "9.8703e-06", no_lofs: String = "124783", obs_het_lof: String = "7", obs_hom_lof: String = "0", defined: String = "124790", p: String = "2.8048e-05", exp_hom_lof: String = "9.8168e-05", classic_caf_afr: String = "8.5353e-05", classic_caf_amr: String = "3.4858e-05", classic_caf_asj: String = "0.0000e+00", classic_caf_eas: String = "0.0000e+00", classic_caf_fin: String = "0.0000e+00", classic_caf_nfe: String = "6.3937e-05", classic_caf_oth: String = "0.0000e+00", classic_caf_sas: String = "6.6100e-05", p_afr: String = "6.4560e-05", p_amr: String = "2.8964e-05", p_asj: String = "0.0000e+00", p_eas: String = "0.0000e+00", p_fin: String = "0.0000e+00", p_nfe: String = "3.5310e-05", p_oth: String = "0.0000e+00", p_sas: String = "3.2678e-05", transcript_type: String = "protein_coding", gene_id: String = "ENSG00000130749", transcript_level: String = "2", cds_length: String = "3909", num_coding_exons: String = "14", gene_type: String = "protein_coding", gene_length: String = "49566", exac_pLI: String = "1.0000e+00", exac_obs_lof: String = "0", exac_exp_lof: String = "4.2170e+01", exac_oe_lof: String = "0.0000e+00", brain_expression: String = "NA", chromosome: String = "19", start_position: String = "47567444", end_position: String = "47617009") extends Product with Serializable
  8. case class RawOmimGeneSet(_c0: String = "chr1", _c1: Int = 2228318, _c2: Int = 2310212, _c3: String = "1p36.3", _c4: String = "1p36.33-p36.32", _c5: Int = 164780, _c6: String = "SKI, SGS", _c7: String = "SKI proto-oncogene", _c8: String = "SKI", _c9: Int = 6497, _c10: String = "ENSG00000157933", _c11: String = "formerly mapped to 1q22-q24", _c12: String = ..., _c13: String = "Ski (MGI:98310)") extends Product with Serializable
  9. case class RawOrphanetProduct6(disorder_id: Long = 21, orpha_code: Long = 447, expert_link: String = ..., name: String = ..., disorder_type_id: Long = 21394, disorder_type_name: String = "Disease", disorder_group_id: Long = 36547, disorder_group_name: String = "Disorder", gene_source_of_validation: String = "22305531[PMID]", gene_id: Long = 19197, gene_symbol: String = "PIGA", gene_name: String = ..., gene_synonym_list: List[String] = ..., ensembl_gene_id: String = "ENSG00000165195", genatlas_gene_id: String = "PIGA", HGNC_gene_id: String = "8957", omim_gene_id: String = "311770", reactome_gene_id: String = "P37287", swiss_prot_gene_id: String = "P37287", association_type: String = ..., association_type_id: Long = 17955, association_status: String = "Assessed", gene_locus_id: Long = 22873, gene_locus: String = "Xp22.2", gene_locus_key: Long = 1) extends Product with Serializable
  10. case class RawOrphanetProduct9(disorder_id: Long = 2, orpha_code: Long = 58, expert_link: String = ..., name: String = "Alexander disease", disorder_type_id: Long = 21394, disorder_type_name: String = "Disease", disorder_group_id: Long = 36547, disorder_group_name: String = "Disease", average_age_of_onset: List[String] = List("All ages"), average_age_of_death: List[String] = List("any age"), type_of_inheritance: List[String] = List("Autosomal dominant")) extends Product with Serializable
  11. case class RawSpliceAi(contigName: String = "1", start: Long = 210862941, end: Long = 210862945, names: Option[Seq[String]] = None, referenceAllele: String = "GGCA", alternateAlleles: Seq[String] = Seq("G"), qual: Option[Double] = None, filters: Option[Seq[String]] = None, splitFromMultiAllelic: Boolean = false, INFO_SpliceAI: Seq[String] = ..., INFO_OLD_MULTIALLELIC: Option[String] = None, genotypes: Seq[GENOTYPES] = Seq(GENOTYPES(sampleId = None))) extends Product with Serializable
  12. case class RawVcf(contigName: String = "chr1", start: Long = 69896, end: Long = 69897, names: List[String] = List("rs200676709"), referenceAllele: String = "T", alternateAlleles: List[String] = List("C"), qual: Double = 2324.17, splitFromMultiAllelic: Boolean = false, INFO_FILTERS: List[String] = List("PASS"), INFO_AC: List[Int] = List(59), INFO_SOR: Double = 0.005, INFO_ReadPosRankSum: Double = 0.736, INFO_AN: Int = 88, INFO_AF: List[Double] = List(0.67), INFO_FS: Double = 57.081, INFO_LOD: Option[Double] = None, INFO_DP: Int = 330, INFO_MQ: Double = 15.54, INFO_QD: Double = 8.07, INFO_END: Option[Int] = None, INFO_CSQ: List[InfoCSQ] = List(InfoCSQ()), INFO_DB: Boolean = true, INFO_MQRankSum: Double = 2.054, INFO_OLD_MULTIALLELIC: Option[String] = None, genotypes: List[SNV_GENOTYPES] = ...) extends Product with Serializable
  13. case class RawVcfWithInfoAnn(contigName: String = "chr1", start: Long = 69896, end: Long = 69897, names: List[String] = List("rs200676709"), referenceAllele: String = "T", alternateAlleles: List[String] = List("C"), qual: Double = 2324.17, splitFromMultiAllelic: Boolean = false, INFO_FILTERS: List[String] = List("PASS"), INFO_AC: List[Int] = List(59), INFO_SOR: Double = 0.005, INFO_ReadPosRankSum: Double = 0.736, INFO_AN: Int = 88, INFO_AF: List[Double] = List(0.67), INFO_FS: Double = 57.081, INFO_LOD: Option[Double] = None, INFO_DP: Int = 330, INFO_MQ: Double = 15.54, INFO_QD: Double = 8.07, INFO_END: Option[Int] = None, INFO_ANN: List[InfoCSQ] = List(InfoCSQ()), INFO_DB: Boolean = true, INFO_MQRankSum: Double = 2.054, INFO_OLD_MULTIALLELIC: Option[String] = None, genotypes: List[SNV_GENOTYPES] = ...) extends Product with Serializable
  14. case class SNV_GENOTYPES(sampleId: String = "11111", conditionalQuality: Int = 30, F1R2: List[Int] = List(0, 0), PRI: Option[List[Double]] = None, filters: List[String] = List("PASS"), posteriorProbabilities: List[Double] = List(7.795, 3.805, 3.795), SB: Option[List[Int]] = None, F2R1: List[Int] = List(0, 1), alleleDepths: List[Int] = List(0, 30), ICNT: Option[List[Int]] = None, AF: List[Double] = List(1.0), phased: Boolean = false, calls: List[Int] = List(0, 1), MIN_DP: Option[Int] = None, phredLikelihoods: List[Int] = List(42, 3, 0), LOD: Option[Double] = None, depth: Int = 1, SPL: Option[List[Int]] = None, PS: Option[Int] = None, MB: Option[List[Int]] = None) extends Product with Serializable

Ungrouped