vep

Version:: 75
Category:: bio
Cluster:: Loki

Author / Distributor

https://useast.ensembl.org/info/docs/tools/vep/index.html

Description

VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.)

Documentation

Usage: vep [OPTIONS]

Variant Effect Predictor (VEP) - analyzes genomic variants.

General options:
  -h, --help             Show this help message and exit
  --version              Display VEP version
  -i, --input_file FILE  Specify input file containing variants
  -o, --output_file FILE Specify output file name
  -f, --format FORMAT    Input file format (vcf, ensembl, pileup, etc.)
  -v, --verbose          Display additional details during execution

Annotation options:
  --cache                Use Ensembl VEP cache
  --database             Retrieve annotation from Ensembl databases
  --species SPECIES      Specify species (default: homo_sapiens)
  --custom FILE          Use custom annotation file

Filtering options:
  --filter FILTER        Apply a filter to annotation results
  --sift [p|s]           Include SIFT prediction (p = score, s = status)
  --polyphen [p|s]       Include PolyPhen prediction (p = score, s = status)

Output options:
  --tab                  Output in tab-delimited format
  --json                 Output in JSON format
  --vcf                  Output in VCF format
  --html                 Output in HTML format

Examples/Usage

Load the VEP module:
```
$ module load vep
```
Check the loaded modules:
```
$ module list
```
List available modules:
```
$ module avail vep
```
Unload the VEP module:
```
$ module unload vep
```

Run VEP on a VCF file:

$ vep -i variants.vcf -o output.txt --cache

Annotate using database mode:

$ vep -i variants.vcf --database --species homo_sapiens -o annotated_variants.txt

Use custom annotation:

$ vep -i variants.vcf --custom my_annotation.bed -o annotated_output.txt

Run VEP with default cache-based annotation:

$ vep --cache --input_file variants.vcf --output_file annotated.txt

Run VEP in database mode:

$ vep --database --input_file variants.vcf --output_file annotated.txt

Output results in VCF format:

$ vep --cache --vcf --input_file variants.vcf --output_file annotated.vcf

Installation

Source code is obtained from Ensembl VEP