annotate_variant_effects_vcf

annotate_variant_effects_vcf annotates the effects of variants on genes in a VCF file. It reads a VCF file and writes a VCF file that has the worst effect, the gene effects and the effect details of each alternative allele in new INFO fields. Use it when you need only the variant effects of a VCF file 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_vcf -gmri hg38/gene_models/MANE/1.4 -rgri hg38/genomes/GRCh38.p14 variants.vcf.gz effects.vcf

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

annotate_variant_effects_vcf -gmfn genes.gtf -gmff gtf -rgfn genome.fa -pl 100 variants.vcf.gz effects.vcf

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

annotate_variant_effects_vcf -gmri hg38/gene_models/MANE/1.4 -rgri hg38/genomes/GRCh38.p14 \
    --annotation-attributes "WE:worst_effect" variants.vcf.gz > effects.vcf

Writes only the WE field, and sends the result to standard output.

Option reference

Annotate Variant Effects in a VCF file.

usage: annotate_variant_effects_vcf [-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]
                                    [--annotation-attributes ANNOTATION_ATTRIBUTES]
                                    input_filename [output_filename]

Positional Arguments

input_filename: input VCF variants file name
output_filename: output file name (default: stdout)

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.

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 : ‘WE:worst_effect,GE:gene_effects,ED:effect_details’.

Default: 'WE:worst_effect,GE:gene_effects,ED:effect_details'