pyxetabase 3.1.0.dev25__py3-none-any.whl → 4.0.0.dev29__py3-none-any.whl

pyopencga/rest_clients/variant_client.py

@@ -1,1378 +0,0 @@
-"""
-WARNING: AUTOGENERATED CODE
-
-    This code was generated by a tool.
-    
-    Manual changes to this file may cause unexpected behavior in your application.
-    Manual changes to this file will be overwritten if the code is regenerated.
-"""
-
-from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
-
-
-class Variant(_ParentRestClient):
-    """
-    This class contains methods for the 'Analysis - Variant' webservices
-    PATH: /{apiVersion}/analysis/variant
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Variant, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def aggregation_stats(self, **options):
-        """
-        Calculate and fetch aggregation stats.
-        PATH: /{apiVersion}/analysis/variant/aggregationStats
-
-        :param str saved_filter: Use a saved filter at User level.
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str type: List of types, accepted values are SNV, MNV, INDEL,
-            SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION,
-            DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g.
-            SNV,INDEL.
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Filter variants from the given studies, these can be
-            either the numeric ID or the alias with the format
-            organization@project:study.
-        :param str cohort: Select variants with calculated stats for the
-            selected cohorts.
-        :param str cohort_stats_ref: Reference Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_alt: Alternate Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_maf: Minor Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_mgf: Minor Genotype Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_pass: Filter PASS frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
-        :param str missing_alleles: Number of missing alleles:
-            [{study:}]{cohort}[<|>|<=|>=]{number}.
-        :param str missing_genotypes: Number of missing genotypes:
-            [{study:}]{cohort}[<|>|<=|>=]{number}.
-        :param str score: Filter by variant score:
-            [{study:}]{score}[<|>|<=|>=]{number}.
-        :param bool annotation_exists: Return only annotated variants.
-        :param str gene: List of genes, most gene IDs are accepted (HGNC,
-            Ensembl gene, ...). This is an alias to 'xref' parameter.
-        :param str ct: List of SO consequence types, e.g.
-            missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts
-            aliases 'loss_of_function' and 'protein_altering'.
-        :param str xref: List of any external reference, these can be genes,
-            proteins or variants. Accepted IDs include HGNC, Ensembl genes,
-            dbSNP, ClinVar, HPO, Cosmic, HGVS ...
-        :param str biotype: List of biotypes, e.g. protein_coding.
-        :param str protein_substitution: Protein substitution scores include
-            SIFT and PolyPhen. You can query using the score
-            {protein_score}[<|>|<=|>=]{number} or the description
-            {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant.
-        :param str conservation: Filter by conservation score:
-            {conservation_score}[<|>|<=|>=]{number} e.g.
-            phastCons>0.5,phylop<0.1,gerp>0.1.
-        :param str population_frequency_alt: Alternate Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str population_frequency_ref: Reference Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str population_frequency_maf: Population minor allele
-            frequency: {study}:{population}[<|>|<=|>=]{number}. e.g.
-            1000G:ALL<0.01.
-        :param str transcript_flag: List of transcript flags. e.g. canonical,
-            CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc,
-            TSO500.
-        :param str gene_trait_id: List of gene trait association id. e.g.
-            'umls:C0007222' , 'OMIM:269600'.
-        :param str go: List of GO (Gene Ontology) terms. e.g. 'GO:0002020'.
-        :param str expression: List of tissues of interest. e.g. 'lung'.
-        :param str protein_keyword: List of Uniprot protein variant annotation
-            keywords.
-        :param str drug: List of drug names.
-        :param str functional_score: Functional score:
-            {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
-            cadd_raw<=0.3.
-        :param str clinical: Clinical source: clinvar, cosmic.
-        :param str clinical_significance: Clinical significance: benign,
-            likely_benign, likely_pathogenic, pathogenic.
-        :param bool clinical_confirmed_status: Clinical confirmed status.
-        :param str custom_annotation: Custom annotation:
-            {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}.
-        :param str trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.:
-            IDs, histologies, descriptions,...
-        :param str field: List of facet fields separated by semicolons, e.g.:
-            studies;type. For nested faceted fields use >>, e.g.:
-            chromosome>>type;percentile(gerp).
-        """
-
-        return self._get(category='analysis', resource='aggregationStats', subcategory='variant', **options)
-
-    def metadata_annotation(self, **options):
-        """
-        Read variant annotations metadata from any saved versions.
-        PATH: /{apiVersion}/analysis/variant/annotation/metadata
-
-        :param str annotation_id: Annotation identifier.
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        """
-
-        return self._get(category='analysis', resource='metadata', subcategory='variant/annotation', **options)
-
-    def query_annotation(self, **options):
-        """
-        Query variant annotations from any saved versions.
-        PATH: /{apiVersion}/analysis/variant/annotation/query
-
-        :param str id: List of variant IDs in the format chrom:start:ref:alt,
-            e.g. 19:7177679:C:T.
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param str annotation_id: Annotation identifier.
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='variant/annotation', **options)
-
-    def run_circos(self, data=None, **options):
-        """
-        Generate a Circos plot for a given sample.
-        PATH: /{apiVersion}/analysis/variant/circos/run
-
-        :param dict data: Circos analysis params to customize the plot. These
-            parameters include the title,  the plot density (i.e., the number
-            of points to display), the general query and the list of tracks.
-            Currently, the supported track types are: COPY-NUMBER, INDEL,
-            REARRANGEMENT and SNV. In addition, each track can contain a
-            specific query. (REQUIRED)
-        :param str study: study.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/circos', data=data, **options)
-
-    def delete_cohort_stats(self, **options):
-        """
-        Delete cohort variant stats from a cohort.
-        PATH: /{apiVersion}/analysis/variant/cohort/stats/delete
-
-        :param str study: study.
-        :param str cohort: Cohort ID or UUID.
-        """
-
-        return self._delete(category='analysis', resource='delete', subcategory='variant/cohort/stats', **options)
-
-    def info_cohort_stats(self, cohort, **options):
-        """
-        Read cohort variant stats from list of cohorts.
-        PATH: /{apiVersion}/analysis/variant/cohort/stats/info
-
-        :param str cohort: Comma separated list of cohort IDs or UUIDs up to a
-            maximum of 100. (REQUIRED)
-        :param str study: study.
-        """
-
-        options['cohort'] = cohort
-        return self._get(category='analysis', resource='info', subcategory='variant/cohort/stats', **options)
-
-    def run_cohort_stats(self, data=None, **options):
-        """
-        Compute cohort variant stats for the selected list of samples.
-        PATH: /{apiVersion}/analysis/variant/cohort/stats/run
-
-        :param dict data: Cohort variant stats params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/cohort/stats', data=data, **options)
-
-    def run_exomiser(self, data=None, **options):
-        """
-        The Exomiser is a Java program that finds potential disease-causing
-            variants from whole-exome or whole-genome sequencing data.
-        PATH: /{apiVersion}/analysis/variant/exomiser/run
-
-        :param dict data: Exomiser parameters. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/exomiser', data=data, **options)
-
-    def run_export(self, data=None, **options):
-        """
-        Filter and export variants from the variant storage to a file.
-        PATH: /{apiVersion}/analysis/variant/export/run
-
-        :param dict data: Variant export params. (REQUIRED)
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/export', data=data, **options)
-
-    def genotypes_family(self, mode_of_inheritance, **options):
-        """
-        Calculate the possible genotypes for the members of a family.
-        PATH: /{apiVersion}/analysis/variant/family/genotypes
-
-        :param str mode_of_inheritance: Mode of inheritance. Allowed values:
-            ['AUTOSOMAL_DOMINANT AUTOSOMAL_RECESSIVE X_LINKED_DOMINANT
-            X_LINKED_RECESSIVE Y_LINKED MITOCHONDRIAL DE_NOVO MENDELIAN_ERROR
-            COMPOUND_HETEROZYGOUS UNKNOWN'] (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str family: Family id.
-        :param str clinical_analysis: Clinical analysis id.
-        :param str penetrance: Penetrance. Allowed values: ['COMPLETE
-            INCOMPLETE UNKNOWN']
-        :param str disorder: Disorder id.
-        """
-
-        options['modeOfInheritance'] = mode_of_inheritance
-        return self._get(category='analysis', resource='genotypes', subcategory='variant/family', **options)
-
-    def run_family_qc(self, data=None, **options):
-        """
-        Run quality control (QC) for a given family. It computes the
-            relatedness scores among the family members.
-        PATH: /{apiVersion}/analysis/variant/family/qc/run
-
-        :param dict data: Family QC analysis params. Family ID. Relatedness
-            method, by default 'PLINK/IBD'. Minor  allele frequence (MAF) is
-            used to filter variants before computing relatedness, e.g.:
-            1000G:CEU>0.35 or cohort:ALL>0.05. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/family/qc', data=data, **options)
-
-    def delete_file(self, **options):
-        """
-         [DEPRECATED] Use operation/variant/delete.
-        PATH: /{apiVersion}/analysis/variant/file/delete
-
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str file: Files to remove.
-        :param bool resume: Resume a previously failed indexation.
-        """
-
-        return self._delete(category='analysis', resource='delete', subcategory='variant/file', **options)
-
-    def run_gatk(self, data=None, **options):
-        """
-        GATK is a Genome Analysis Toolkit for variant discovery in
-            high-throughput sequencing data. Supported Gatk commands:
-            HaplotypeCaller.
-        PATH: /{apiVersion}/analysis/variant/gatk/run
-
-        :param dict data: Gatk parameters. Supported Gatk commands:
-            HaplotypeCaller. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/gatk', data=data, **options)
-
-    def run_genome_plot(self, data=None, **options):
-        """
-        Generate a genome plot for a given sample.
-        PATH: /{apiVersion}/analysis/variant/genomePlot/run
-
-        :param dict data: Genome plot analysis params to customize the plot.
-            The configuration file includes the title,  the plot density (i.e.,
-            the number of points to display), the general query and the list of
-            tracks. Currently, the supported track types are: COPY-NUMBER,
-            INDEL, REARRANGEMENT and SNV. In addition, each track can contain a
-            specific query. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/genomePlot', data=data, **options)
-
-    def run_gwas(self, data=None, **options):
-        """
-        Run a Genome Wide Association Study between two cohorts.
-        PATH: /{apiVersion}/analysis/variant/gwas/run
-
-        :param dict data: Gwas analysis params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/gwas', data=data, **options)
-
-    def run_hr_detect(self, data=None, **options):
-        """
-        Run HRDetect analysis for a given somatic sample.
-        PATH: /{apiVersion}/analysis/variant/hrDetect/run
-
-        :param dict data: HRDetect analysis parameters. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/hrDetect', data=data, **options)
-
-    def run_index(self, data=None, **options):
-        """
-         [DEPRECATED] Use operation/variant/index.
-        PATH: /{apiVersion}/analysis/variant/index/run
-
-        :param dict data: Variant index params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/index', data=data, **options)
-
-    def run_individual_qc(self, data=None, **options):
-        """
-        Run quality control (QC) for a given individual. It includes inferred
-            sex and  mendelian errors (UDP).
-        PATH: /{apiVersion}/analysis/variant/individual/qc/run
-
-        :param dict data: Individual QC analysis params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/individual/qc', data=data, **options)
-
-    def run_inferred_sex(self, data=None, **options):
-        """
-        Infer sex from chromosome mean coverages.
-        PATH: /{apiVersion}/analysis/variant/inferredSex/run
-
-        :param dict data: Inferred sex analysis params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/inferredSex', data=data, **options)
-
-    def query_knockout_gene(self, **options):
-        """
-        Fetch values from KnockoutAnalysis result, by genes.
-        PATH: /{apiVersion}/analysis/variant/knockout/gene/query
-
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param str study: study.
-        :param str job: Job ID or UUID.
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='variant/knockout/gene', **options)
-
-    def query_knockout_individual(self, **options):
-        """
-        Fetch values from KnockoutAnalysis result, by individuals.
-        PATH: /{apiVersion}/analysis/variant/knockout/individual/query
-
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param str study: study.
-        :param str job: Job ID or UUID.
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='variant/knockout/individual', **options)
-
-    def run_knockout(self, data=None, **options):
-        """
-        Obtains the list of knocked out genes for each sample.
-        PATH: /{apiVersion}/analysis/variant/knockout/run
-
-        :param dict data: Gene knockout analysis params. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/knockout', data=data, **options)
-
-    def run_liftover(self, data=None, **options):
-        """
-        BCFtools liftover plugin maps coordinates from assembly 37 to 38.
-        PATH: /{apiVersion}/analysis/variant/liftover/run
-
-        :param dict data: BCFtools +liftover plugin parameters. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/liftover', data=data, **options)
-
-    def run_mendelian_error(self, data=None, **options):
-        """
-        Run mendelian error analysis to infer uniparental disomy regions.
-        PATH: /{apiVersion}/analysis/variant/mendelianError/run
-
-        :param dict data: Mendelian error analysis params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/mendelianError', data=data, **options)
-
-    def metadata(self, **options):
-        """
-        .
-        PATH: /{apiVersion}/analysis/variant/metadata
-
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Filter variants from the given studies, these can be
-            either the numeric ID or the alias with the format
-            organization@project:study.
-        :param str file: Filter variants from the files specified. This will
-            set includeFile parameter when not provided.
-        :param str sample: Filter variants by sample genotype. This will
-            automatically set 'includeSample' parameter when not provided. This
-            filter accepts multiple 3 forms: 1) List of samples: Samples that
-            contain the main variant. Accepts AND ';' and OR ',' operators. 
-            e.g. HG0097,HG0098 . 2) List of samples with genotypes:
-            {sample}:{gt1},{gt2}. Accepts AND ';' and OR ',' operators.  e.g.
-            HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will
-            also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice
-            versa. When filtering by multi-allelic genotypes, any secondary
-            allele will match, regardless of its position e.g. 1/2 will match
-            with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted:
-            HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS  e.g.
-            HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation
-            mode: {sample}:{segregation}. Only one sample accepted.Accepted
-            segregation modes: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case
-            insensitive. e.g. HG0097:DeNovo Sample must have parents defined
-            and indexed. .
-        :param str include_study: List of studies to include in the result.
-            Accepts 'all' and 'none'.
-        :param str include_file: List of files to be returned. Accepts 'all'
-            and 'none'. If undefined, automatically includes files used for
-            filtering. If none, no file is included.
-        :param str include_sample: List of samples to be included in the
-            result. Accepts 'all' and 'none'. If undefined, automatically
-            includes samples used for filtering. If none, no sample is
-            included.
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        """
-
-        return self._get(category='analysis', resource='metadata', subcategory='variant', **options)
-
-    def query_mutational_signature(self, **options):
-        """
-        Run mutational signature analysis for a given sample. Use context
-            index.
-        PATH: /{apiVersion}/analysis/variant/mutationalSignature/query
-
-        :param str study: Filter variants from the given studies, these can be
-            either the numeric ID or the alias with the format
-            organization@project:study.
-        :param str sample: Sample name.
-        :param str type: Variant type. Valid values: SNV, SV.
-        :param str ct: List of SO consequence types, e.g.
-            missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts
-            aliases 'loss_of_function' and 'protein_altering'.
-        :param str biotype: List of biotypes, e.g. protein_coding.
-        :param str file_data: Filter by file data (i.e. FILTER, QUAL and INFO
-            columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file
-            is specified, will use all files from 'file' filter. e.g. AN>200 or
-            file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined.
-            e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP.
-        :param str filter: Specify the FILTER for any of the files. If 'file'
-            filter is provided, will match the file and the filter. e.g.:
-            PASS,LowGQX.
-        :param str qual: Specify the QUAL for any of the files. If 'file'
-            filter is provided, will match the file and the qual. e.g.: >123.4.
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str gene: List of genes, most gene IDs are accepted (HGNC,
-            Ensembl gene, ...). This is an alias to 'xref' parameter.
-        :param str panel: Filter by genes from the given disease panel.
-        :param str panel_mode_of_inheritance: Filter genes from specific
-            panels that match certain mode of inheritance. Accepted values : [
-            autosomalDominant, autosomalRecessive, XLinkedDominant,
-            XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError,
-            compoundHeterozygous ].
-        :param str panel_confidence: Filter genes from specific panels that
-            match certain confidence. Accepted values : [ high, medium, low,
-            rejected ].
-        :param str panel_feature_type: Filter elements from specific panels by
-            type. Accepted values : [ gene, region, str, variant ].
-        :param str panel_role_in_cancer: Filter genes from specific panels
-            that match certain role in cancer. Accepted values : [ both,
-            oncogene, tumorSuppressorGene, fusion ].
-        :param bool panel_intersection: Intersect panel genes and regions with
-            given genes and regions from que input query. This will prevent
-            returning variants from regions out of the panel.
-        :param str ms_id: Signature ID.
-        :param str ms_description: Signature description.
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='variant/mutationalSignature', **options)
-
-    def run_mutational_signature(self, data=None, **options):
-        """
-        Run mutational signature analysis for a given sample.
-        PATH: /{apiVersion}/analysis/variant/mutationalSignature/run
-
-        :param dict data: Mutational signature analysis parameters to index
-            the genome context for that sample, and to compute both catalogue
-            counts and signature fitting. In order to skip one of them, , use
-            the following keywords: , catalogue, fitting. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/mutationalSignature', data=data, **options)
-
-    def run_plink(self, data=None, **options):
-        """
-        Plink is a whole genome association analysis toolset, designed to
-            perform a range of basic, large-scale analyses.
-        PATH: /{apiVersion}/analysis/variant/plink/run
-
-        :param dict data: Plink params. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/plink', data=data, **options)
-
-    def query(self, **options):
-        """
-        Filter and fetch variants from indexed VCF files in the variant
-            storage.
-        PATH: /{apiVersion}/analysis/variant/query
-
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param bool count: Get the total number of results matching the query.
-            Deactivated by default.
-        :param bool sort: Sort the results.
-        :param bool summary: Fast fetch of main variant parameters.
-        :param bool approximate_count: Get an approximate count, instead of an
-            exact total count. Reduces execution time.
-        :param int approximate_count_sampling_size: Sampling size to get the
-            approximate count. Larger values increase accuracy but also
-            increase execution time.
-        :param str saved_filter: Use a saved filter at User level.
-        :param str id: List of variant IDs in the format chrom:start:ref:alt,
-            e.g. 19:7177679:C:T.
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str type: List of types, accepted values are SNV, MNV, INDEL,
-            SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION,
-            DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g.
-            SNV,INDEL.
-        :param str reference: Reference allele.
-        :param str alternate: Main alternate allele.
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Filter variants from the given studies, these can be
-            either the numeric ID or the alias with the format
-            organization@project:study.
-        :param str file: Filter variants from the files specified. This will
-            set includeFile parameter when not provided.
-        :param str filter: Specify the FILTER for any of the files. If 'file'
-            filter is provided, will match the file and the filter. e.g.:
-            PASS,LowGQX.
-        :param str qual: Specify the QUAL for any of the files. If 'file'
-            filter is provided, will match the file and the qual. e.g.: >123.4.
-        :param str file_data: Filter by file data (i.e. FILTER, QUAL and INFO
-            columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file
-            is specified, will use all files from 'file' filter. e.g. AN>200 or
-            file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined.
-            e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP.
-        :param str sample: Filter variants by sample genotype. This will
-            automatically set 'includeSample' parameter when not provided. This
-            filter accepts multiple 3 forms: 1) List of samples: Samples that
-            contain the main variant. Accepts AND ';' and OR ',' operators. 
-            e.g. HG0097,HG0098 . 2) List of samples with genotypes:
-            {sample}:{gt1},{gt2}. Accepts AND ';' and OR ',' operators.  e.g.
-            HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will
-            also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice
-            versa. When filtering by multi-allelic genotypes, any secondary
-            allele will match, regardless of its position e.g. 1/2 will match
-            with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted:
-            HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS  e.g.
-            HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation
-            mode: {sample}:{segregation}. Only one sample accepted.Accepted
-            segregation modes: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case
-            insensitive. e.g. HG0097:DeNovo Sample must have parents defined
-            and indexed. .
-        :param str genotype: Samples with a specific genotype:
-            {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g.
-            HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will
-            also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice
-            versa. When filtering by multi-allelic genotypes, any secondary
-            allele will match, regardless of its position e.g. 1/2 will match
-            with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted:
-            HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS  e.g.
-            HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT. This will automatically set
-            'includeSample' parameter when not provided.
-        :param str sample_data: Filter by any SampleData field from samples.
-            [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will
-            use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or
-            HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined.
-            e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10.
-        :param str sample_annotation: Selects some samples using metadata
-            information from Catalog. e.g.
-            age>20;phenotype=hpo:123,hpo:456;name=smith.
-        :param bool sample_metadata: Return the samples metadata group by
-            study. Sample names will appear in the same order as their
-            corresponding genotypes.
-        :param str unknown_genotype: Returned genotype for unknown genotypes.
-            Common values: [0/0, 0|0, ./.].
-        :param int sample_limit: Limit the number of samples to be included in
-            the result.
-        :param int sample_skip: Skip some samples from the result. Useful for
-            sample pagination.
-        :param str cohort: Select variants with calculated stats for the
-            selected cohorts.
-        :param str cohort_stats_ref: Reference Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_alt: Alternate Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_maf: Minor Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_mgf: Minor Genotype Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_pass: Filter PASS frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
-        :param str missing_alleles: Number of missing alleles:
-            [{study:}]{cohort}[<|>|<=|>=]{number}.
-        :param str missing_genotypes: Number of missing genotypes:
-            [{study:}]{cohort}[<|>|<=|>=]{number}.
-        :param str score: Filter by variant score:
-            [{study:}]{score}[<|>|<=|>=]{number}.
-        :param str family: Filter variants where any of the samples from the
-            given family contains the variant (HET or HOM_ALT).
-        :param str family_disorder: Specify the disorder to use for the family
-            segregation.
-        :param str family_segregation: Filter by segregation mode from a given
-            family. Accepted values: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ].
-        :param str family_members: Sub set of the members of a given family.
-        :param str family_proband: Specify the proband child to use for the
-            family segregation.
-        :param str include_study: List of studies to include in the result.
-            Accepts 'all' and 'none'.
-        :param str include_file: List of files to be returned. Accepts 'all'
-            and 'none'. If undefined, automatically includes files used for
-            filtering. If none, no file is included.
-        :param str include_sample: List of samples to be included in the
-            result. Accepts 'all' and 'none'. If undefined, automatically
-            includes samples used for filtering. If none, no sample is
-            included.
-        :param str include_sample_data: List of Sample Data keys (i.e. FORMAT
-            column from VCF file) from Sample Data to include in the output.
-            e.g: DP,AD. Accepts 'all' and 'none'.
-        :param str include_genotype: Include genotypes, apart of other formats
-            defined with includeFormat.
-        :param str include_sample_id: Include sampleId on each result.
-        :param bool annotation_exists: Return only annotated variants.
-        :param str gene: List of genes, most gene IDs are accepted (HGNC,
-            Ensembl gene, ...). This is an alias to 'xref' parameter.
-        :param str ct: List of SO consequence types, e.g.
-            missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts
-            aliases 'loss_of_function' and 'protein_altering'.
-        :param str xref: List of any external reference, these can be genes,
-            proteins or variants. Accepted IDs include HGNC, Ensembl genes,
-            dbSNP, ClinVar, HPO, Cosmic, HGVS ...
-        :param str biotype: List of biotypes, e.g. protein_coding.
-        :param str protein_substitution: Protein substitution scores include
-            SIFT and PolyPhen. You can query using the score
-            {protein_score}[<|>|<=|>=]{number} or the description
-            {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant.
-        :param str conservation: Filter by conservation score:
-            {conservation_score}[<|>|<=|>=]{number} e.g.
-            phastCons>0.5,phylop<0.1,gerp>0.1.
-        :param str population_frequency_alt: Alternate Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str population_frequency_ref: Reference Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str population_frequency_maf: Population minor allele
-            frequency: {study}:{population}[<|>|<=|>=]{number}. e.g.
-            1000G:ALL<0.01.
-        :param str transcript_flag: List of transcript flags. e.g. canonical,
-            CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc,
-            TSO500.
-        :param str gene_trait_id: List of gene trait association id. e.g.
-            'umls:C0007222' , 'OMIM:269600'.
-        :param str go: List of GO (Gene Ontology) terms. e.g. 'GO:0002020'.
-        :param str expression: List of tissues of interest. e.g. 'lung'.
-        :param str protein_keyword: List of Uniprot protein variant annotation
-            keywords.
-        :param str drug: List of drug names.
-        :param str functional_score: Functional score:
-            {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
-            cadd_raw<=0.3.
-        :param str clinical: Clinical source: clinvar, cosmic.
-        :param str clinical_significance: Clinical significance: benign,
-            likely_benign, likely_pathogenic, pathogenic.
-        :param bool clinical_confirmed_status: Clinical confirmed status.
-        :param str custom_annotation: Custom annotation:
-            {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}.
-        :param str panel: Filter by genes from the given disease panel.
-        :param str panel_mode_of_inheritance: Filter genes from specific
-            panels that match certain mode of inheritance. Accepted values : [
-            autosomalDominant, autosomalRecessive, XLinkedDominant,
-            XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError,
-            compoundHeterozygous ].
-        :param str panel_confidence: Filter genes from specific panels that
-            match certain confidence. Accepted values : [ high, medium, low,
-            rejected ].
-        :param str panel_role_in_cancer: Filter genes from specific panels
-            that match certain role in cancer. Accepted values : [ both,
-            oncogene, tumorSuppressorGene, fusion ].
-        :param str panel_feature_type: Filter elements from specific panels by
-            type. Accepted values : [ gene, region, str, variant ].
-        :param bool panel_intersection: Intersect panel genes and regions with
-            given genes and regions from que input query. This will prevent
-            returning variants from regions out of the panel.
-        :param str source: Select the variant data source from where to fetch
-            the data. Accepted values are 'variant_index' (default) and
-            'secondary_sample_index'. When selecting a secondary_index, the
-            data will be retrieved exclusively from that secondary index, and
-            the 'include/exclude' parameters will be ignored. If the given
-            query can not be fully resolved using the secondary index, an
-            exception will be raised. As the returned variants will only
-            contain data from the secondary_index, some data might be missing
-            or be partial.
-        :param str trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.:
-            IDs, histologies, descriptions,...
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='variant', **options)
-
-    def run_relatedness(self, data=None, **options):
-        """
-        Compute a score to quantify relatedness between samples.
-        PATH: /{apiVersion}/analysis/variant/relatedness/run
-
-        :param dict data: Relatedness analysis params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/relatedness', data=data, **options)
-
-    def run_rvtests(self, data=None, **options):
-        """
-        Rvtests is a flexible software package for genetic association
-            studies. Supported RvTests commands: rvtest, vcf2kinship.
-        PATH: /{apiVersion}/analysis/variant/rvtests/run
-
-        :param dict data: RvTests parameters. Supported RvTests commands:
-            rvtest, vcf2kinship. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/rvtests', data=data, **options)
-
-    def aggregation_stats_sample(self, **options):
-        """
-        Calculate and fetch sample aggregation stats.
-        PATH: /{apiVersion}/analysis/variant/sample/aggregationStats
-
-        :param str saved_filter: Use a saved filter at User level.
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str type: List of types, accepted values are SNV, MNV, INDEL,
-            SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION,
-            DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g.
-            SNV,INDEL.
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Filter variants from the given studies, these can be
-            either the numeric ID or the alias with the format
-            organization@project:study.
-        :param str file: Filter variants from the files specified. This will
-            set includeFile parameter when not provided.
-        :param str filter: Specify the FILTER for any of the files. If 'file'
-            filter is provided, will match the file and the filter. e.g.:
-            PASS,LowGQX.
-        :param str sample: Filter variants by sample genotype. This will
-            automatically set 'includeSample' parameter when not provided. This
-            filter accepts multiple 3 forms: 1) List of samples: Samples that
-            contain the main variant. Accepts AND ';' and OR ',' operators. 
-            e.g. HG0097,HG0098 . 2) List of samples with genotypes:
-            {sample}:{gt1},{gt2}. Accepts AND ';' and OR ',' operators.  e.g.
-            HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will
-            also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice
-            versa. When filtering by multi-allelic genotypes, any secondary
-            allele will match, regardless of its position e.g. 1/2 will match
-            with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted:
-            HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS  e.g.
-            HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation
-            mode: {sample}:{segregation}. Only one sample accepted.Accepted
-            segregation modes: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case
-            insensitive. e.g. HG0097:DeNovo Sample must have parents defined
-            and indexed. .
-        :param str genotype: Samples with a specific genotype:
-            {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g.
-            HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will
-            also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice
-            versa. When filtering by multi-allelic genotypes, any secondary
-            allele will match, regardless of its position e.g. 1/2 will match
-            with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted:
-            HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS  e.g.
-            HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT. This will automatically set
-            'includeSample' parameter when not provided.
-        :param str sample_annotation: Selects some samples using metadata
-            information from Catalog. e.g.
-            age>20;phenotype=hpo:123,hpo:456;name=smith.
-        :param str family: Filter variants where any of the samples from the
-            given family contains the variant (HET or HOM_ALT).
-        :param str family_disorder: Specify the disorder to use for the family
-            segregation.
-        :param str family_segregation: Filter by segregation mode from a given
-            family. Accepted values: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ].
-        :param str family_members: Sub set of the members of a given family.
-        :param str family_proband: Specify the proband child to use for the
-            family segregation.
-        :param str ct: List of SO consequence types, e.g.
-            missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts
-            aliases 'loss_of_function' and 'protein_altering'.
-        :param str biotype: List of biotypes, e.g. protein_coding.
-        :param str population_frequency_alt: Alternate Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str clinical: Clinical source: clinvar, cosmic.
-        :param str clinical_significance: Clinical significance: benign,
-            likely_benign, likely_pathogenic, pathogenic.
-        :param bool clinical_confirmed_status: Clinical confirmed status.
-        :param str field: List of facet fields separated by semicolons, e.g.:
-            studies;type. For nested faceted fields use >>, e.g.:
-            chromosome>>type . Accepted values: chromosome, type, genotype,
-            consequenceType, biotype, clinicalSignificance, dp, qual, filter.
-        """
-
-        return self._get(category='analysis', resource='aggregationStats', subcategory='variant/sample', **options)
-
-    def run_sample_eligibility(self, data=None, **options):
-        """
-        Filter samples by a complex query involving metadata and variants
-            data.
-        PATH: /{apiVersion}/analysis/variant/sample/eligibility/run
-
-        :param dict data: . (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/sample/eligibility', data=data, **options)
-
-    def run_sample_qc(self, data=None, **options):
-        """
-        Run quality control (QC) for a given sample. It includes variant
-            stats, and if the sample is somatic, mutational signature and
-            genome plot are calculated.
-        PATH: /{apiVersion}/analysis/variant/sample/qc/run
-
-        :param dict data: Sample QC analysis params. Mutational signature and
-            genome plot are calculated for somatic samples only. In order to
-            skip some metrics, use the following keywords (separated by
-            commas): variant-stats, signature, signature-catalogue,
-            signature-fitting, genome-plot. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/sample/qc', data=data, **options)
-
-    def query_sample(self, **options):
-        """
-        Get sample data of a given variant.
-        PATH: /{apiVersion}/analysis/variant/sample/query
-
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param str variant: Variant.
-        :param str study: Study where all the samples belong to.
-        :param str genotype: Genotypes that the sample must have to be
-            selected.
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='variant/sample', **options)
-
-    def run_sample(self, data=None, **options):
-        """
-        Get samples given a set of variants.
-        PATH: /{apiVersion}/analysis/variant/sample/run
-
-        :param dict data: Sample variant filter params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/sample', data=data, **options)
-
-    def query_sample_stats(self, sample, **options):
-        """
-        Obtain sample variant stats from a sample.
-        PATH: /{apiVersion}/analysis/variant/sample/stats/query
-
-        :param str sample: Sample ID. (REQUIRED)
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str type: List of types, accepted values are SNV, MNV, INDEL,
-            SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION,
-            DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g.
-            SNV,INDEL.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str file: Filter variants from the files specified. This will
-            set includeFile parameter when not provided.
-        :param str filter: Specify the FILTER for any of the files. If 'file'
-            filter is provided, will match the file and the filter. e.g.:
-            PASS,LowGQX.
-        :param str sample_data: Filter by any SampleData field from samples.
-            [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will
-            use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or
-            HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined.
-            e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10.
-        :param str ct: List of SO consequence types, e.g.
-            missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts
-            aliases 'loss_of_function' and 'protein_altering'.
-        :param str biotype: List of biotypes, e.g. protein_coding.
-        :param str transcript_flag: List of transcript flags. e.g. canonical,
-            CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc,
-            TSO500.
-        :param str population_frequency_alt: Alternate Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str clinical: Clinical source: clinvar, cosmic.
-        :param str clinical_significance: Clinical significance: benign,
-            likely_benign, likely_pathogenic, pathogenic.
-        :param bool clinical_confirmed_status: Clinical confirmed status.
-        :param bool filter_transcript: Do filter transcripts when obtaining
-            transcript counts.
-        """
-
-        options['sample'] = sample
-        return self._get(category='analysis', resource='query', subcategory='variant/sample/stats', **options)
-
-    def run_sample_stats(self, data=None, **options):
-        """
-        Compute sample variant stats for the selected list of samples.
-        PATH: /{apiVersion}/analysis/variant/sample/stats/run
-
-        :param dict data: Sample variant stats params. Use index=true and
-            indexId='' to store the result in catalog sample QC. indexId=ALL
-            requires an empty query. Use sample=all to compute sample stats of
-            all samples in the variant storage. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/sample/stats', data=data, **options)
-
-    def run_stats_export(self, data=None, **options):
-        """
-        Export calculated variant stats and frequencies.
-        PATH: /{apiVersion}/analysis/variant/stats/export/run
-
-        :param dict data: Variant stats export params. (REQUIRED)
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/stats/export', data=data, **options)
-
-    def run_stats(self, data=None, **options):
-        """
-        Compute variant stats for any cohort and any set of variants.
-        PATH: /{apiVersion}/analysis/variant/stats/run
-
-        :param dict data: Variant stats params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/stats', data=data, **options)
-
-    def run_walker(self, data=None, **options):
-        """
-        Filter and walk variants from the variant storage to produce a file.
-        PATH: /{apiVersion}/analysis/variant/walker/run
-
-        :param dict data: Variant walker params. (REQUIRED)
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='variant/walker', data=data, **options)
-