Type Members

1.  case class Consequences(rc: RuntimeETLContext) extends SimpleSingleETL with Product with Serializable
2.  case class UpdateClinvarVariants(rc: RuntimeETLContext) extends SimpleSingleETL with Product with Serializable

   This ETL update column clinvar in variants table with latest version of clinvar table

   This ETL update column clinvar in variants table with latest version of clinvar table

   rc

   the etl context

3.  case class Variants(rc: RuntimeETLContext, participantId: Column = col("participant_id"), affectedStatus: Column = col("affected_status"), filterSnv: Option[Column] = Some(col("has_alt")), snvDatasetId: String, splits: Seq[OccurrenceSplit], extraAggregations: Seq[Column] = Nil, checkpoint: Boolean = false, spliceAi: Boolean = true, destinationDataSetId: String = "enriched_variants") extends SimpleSingleETL with Product with Serializable

   This ETL create an aggregated table on occurrences of SNV variants.

   This ETL create an aggregated table on occurrences of SNV variants. Occurrences are aggregated by calculating the frequencies specified in parameter frequencies. The table is enriched with information from other datasets such as genes, dbsnp, clinvar, 1000 genomes, topmed_bravo, gnomad_genomes_v2, gnomad_exomes_v2, gnomad_genomes_v3.

   rc

   the etl context

   participantId

   column used to distinct participants in order to calculate total number of participants (pn) and total allele number (an)

   affectedStatus

   column used to calculate frequencies for affected / unaffected participants

   snvDatasetId

   the id of the dataset containing the SNV variants

   extraAggregations

   extra aggregations to be computed when grouping occurrences by locus. Will be added to the root of the data

   spliceAi

   bool indicating whether or not to join variants with SpliceAI. Defaults to true.