.. _annotation: Annotation Configuration ======================== Annotation config files follow the INI file format and specify a list of annotators and their options in the form of sections and properties. The ``annotation.conf`` file which can be found in the data repository is the default annotation config. Each annotator is described in a single section. The name of the section must be unique, but since it does not influence the annotation process, it can be chosen freely. Lines starting with ``#`` are ignored. All annotators are configured in a similar manner, using three main properties - ``annotator``, ``options`` and ``columns``. ``annotator`` has a single value, but the other two properties have sub-properties separated with a ``.``. Example Configuration --------------------- .. code-block:: ini [DEFAULT] GENOMIC_SCORES_HG19 = %(scores_hg19_dir)s ############################### [Step-CADD-Score] annotator = score_annotator.NPScoreAnnotator options.scores_file = %(GENOMIC_SCORES_HG19)s/CADD/CADD.bedgraph.gz columns.raw = cadd_raw columns.phred = cadd_phred ############################### [Step-MPC-Score] annotator = score_annotator.NPScoreAnnotator options.scores_file = %(GENOMIC_SCORES_HG19)s/MPC/fordist_constraint_official_mpc_values_v2.txt.gz columns.MPC = mpc ####################################### [gnomAD genome Frequency] annotator = frequency_annotator.FrequencyAnnotator options.scores_file = %(GENOMIC_SCORES_HG19)s/gnomAD_genome/gnomad.genomes.r2.1.sites.tsv.gz columns.AF = genome_gnomad_af columns.AF_percent = genome_gnomad_af_percent columns.AC = genome_gnomad_ac columns.AN = genome_gnomad_an columns.controls_AC = genome_gnomad_controls_ac columns.controls_AN = genome_gnomad_controls_an columns.controls_AF = genome_gnomad_controls_af columns.non_neuro_AC = genome_gnomad_non_neuro_ac columns.non_neuro_AN = genome_gnomad_non_neuro_an columns.non_neuro_AF = genome_gnomad_non_neuro_af columns.controls_AF_percent = genome_gnomad_controls_af_percent columns.non_neuro_AF_percent = genome_gnomad_non_neuro_af_percent ####################################### [gnomAD exome Frequency] annotator = frequency_annotator.FrequencyAnnotator options.scores_file = %(GENOMIC_SCORES_HG19)s/gnomAD_exome/gnomad.exomes.r2.1.sites.tsv.gz columns.AF = exome_gnomad_af columns.AF_percent = exome_gnomad_af_percent columns.AC = exome_gnomad_ac columns.AN = exome_gnomad_an columns.controls_AC = exome_gnomad_controls_ac columns.controls_AN = exome_gnomad_controls_an columns.controls_AF = exome_gnomad_controls_af columns.non_neuro_AC = exome_gnomad_non_neuro_ac columns.non_neuro_AN = exome_gnomad_non_neuro_an columns.non_neuro_AF = exome_gnomad_non_neuro_af columns.controls_AF_percent = exome_gnomad_controls_af_percent columns.non_neuro_AF_percent = exome_gnomad_non_neuro_af_percent annotator --------- .. code-block:: ini annotator = . This property indicates the type of the annotator. =========================================== =================================== Value Description =========================================== =================================== annotator_base.CopyAnnotator Duplicates the given columns. cleanup_annotator.CleanupAnnotator Removes the given columns from the output file. dbnsfp_annotator.dbNSFPAnnotator Annotate variants using scores from dbNSFP. effect_annotator.VariantEffectAnnotator Annotate variants with their effects. frequency_annotator.FrequencyAnnotator Annotate variants with a frequency score. score_annotator.PositionScoreAnnotator Annotate variants with a score file by the position/location of the variant. score_annotator.PositionMultiScoreAnnotator Identical in function to PositionScoreAnnotator, but uses a directory with multiple score files. score_annotator.NPScoreAnnotator Annotate variants with a score file by the location *and* the type of the variant. lift_over_annotator.LiftOverAnnotator Create a column with the variant's location lifted over. vcf_info_extractor.VCFInfoExtractor Extract key-value pairs from a VCF file's INFO column as separate columns. =========================================== =================================== options.* --------- .. code-block:: ini options.