annotate_variant_effects

annotate_variant_effects annotates the effects of variants on genes. It reads a delimited text file with one variant on each line, from a file or from standard input. It writes the same file with extra columns for the worst effect, the gene effects and the effect details. Use it when you need only the variant effects of a variant table and you do not want to write an annotation pipeline. The effect_annotator of an annotation pipeline, which annotate_tabular or annotate_vcf runs, computes the same effects. It runs together with the other annotators of the pipeline and takes its configuration from the pipeline file.

Examples

annotate_variant_effects -gmri hg38/gene_models/MANE/1.4 -rgri hg38/genomes/GRCh38.p14 variants.tsv effects.tsv

Selects the gene models and the reference genome by GRR resource id, and annotates the variants of variants.tsv.

annotate_variant_effects -gmfn genes.gtf -gmff gtf -rgfn genome.fa -pl 100 variants.tsv effects.tsv

Selects the gene models and the reference genome by file name, and counts a promoter of 100 base pairs.

annotate_variant_effects -gmri hg38/gene_models/MANE/1.4 -rgri hg38/genomes/GRCh38.p14 \
    --input-sep , --annotation-attributes "WE:worst_effect,GE:gene_effects" variants.csv effects.tsv

Reads a comma-separated file and writes two columns with the names WE and GE.

Option reference

Annotate Variant Effects in a Column File.

usage: annotate_variant_effects [-h] [--verbose] [--logfile LOGFILE]
                                [-grr GENOMIC_REPOSITORY_CONFIG_FILENAME]
                                [-gmfn GENE_MODELS_FILENAME]
                                [-gmff GENE_MODELS_FILEFORMAT]
                                [-gmmfn GENE_MAPPING_FILENAME]
                                [-gmri GENE_MODELS_RESOURCE_ID]
                                [-rgfn REFERENCE_GENOME_FILENAME]
                                [-rgri REFERENCE_GENOME_RESOURCE_ID]
                                [-pl PROMOTER_LEN] [--chrom-col CHROM_COL]
                                [--pos-col POS_COL]
                                [--location-col LOCATION_COL]
                                [--variant-col VARIANT_COL]
                                [--ref-col REF_COL] [--alt-col ALT_COL]
                                [--input-sep INPUT_SEP]
                                [--output-sep OUTPUT_SEP]
                                [--annotation-attributes ANNOTATION_ATTRIBUTES]
                                [input_filename] [output_filename]

Named Arguments

--verbose, -v, -V

Default: 0

--logfile

File to log output to. If not set, logs to console.

-pl, --promoter-len

promoter length: the number of bases upstream of the first exon that count as promoter (0 disables promoter calls)

Default: 0

Genomic repository options

-grr, --genomic-repository-config-filename: Genomic Repository Configuraiton File

Gene models file options

-gmfn, --gene-models-filename: Gene models file name.
-gmff, --gene-models-fileformat: Gene models file format.
-gmmfn, --gene-mapping-filename: Gene mapping file.

Gene models resource options

-gmri, --gene-models-resource-id: Gene models resource id.

Reference genome file options

-rgfn, --reference-genome-filename: Reference genome file name.

Reference genome resource options

-rgri, --reference-genome-resource-id: Reference genome resource id.

Variant columns

--chrom-col: Default: 'chrom'
--pos-col: Default: 'pos'
--location-col: Default: 'location'
--variant-col: Default: 'variant'
--ref-col: Default: 'ref'
--alt-col: Default: 'alt'

Input file

input_filename: Default: '-'
--input-sep: Default: ' '

Output file

output_filename: Default: '-'
--output-sep: Default: ' '

Annotation attributes.

--annotation-attributes

The available attributes are worst_effect, gene_effects, and effect_details. Examples: 1. ‘worst_effect, gene_effects’;2. ‘WE: worst_effect, GE: gene_effects, ED: effect_details’The default is : ‘worst_effect,gene_effects,effect_details’.

Default: 'worst_effect,gene_effects,effect_details'