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Annotation

Tools

With Sarek, annotation is done using snpEff, VEP, or even both consecutively:

  • --tools snpEff
    • To annotate using snpEff
  • --tools VEP
    • To annotate using VEP
  • --tools snpEff,VEP
    • To annotate using snpEff and VEP
  • --tools merge
    • To annotate using snpEff followed by VEP

VCF produced by Sarek will be annotated if snpEff or VEP are specified with the --tools command. As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.

In these examples, all command lines will be launched starting with step annotate. It can of course be started directly from any other step instead.

Using genome specific containers

Sarek has already designed containers with snpEff and VEP files for GRCh37, GRCh38 and GRCm38. Default settings will run using these containers.

The main Sarek container has also snpEff and VEP installed, but without the cache files that can be downloaded separately.

Using downloaded cache

Both snpEff and VEP enable usage of cache. If cache is available on the machine where Sarek is run, it is possible to run annotation using cache. You need to specify the cache directory using --snpEff_cache and --vep_cache in the command lines or within configuration files. The cache will only be used when --annotation_cache and cache directories are specified (either in command lines or in a configuration file).

Example:

nextflow run nf-core/sarek --tools snpEff --step annotate --sample file.vcf.gz --snpEff_cache /Path/To/snpEffCache --annotation_cache
nextflow run nf-core/sarek --tools VEP --step annotate --sample file.vcf.gz --vep_cache /Path/To/vepCache --annotation_cache

Using VEP CADD plugin

To enable the use of the VEP CADD plugin:

  • Download the CADD files
  • Specify them (either on the command line, like in the example or in a configuration file)
  • use the --cadd_cache flag

Example:

nextflow run nf-core/sarek --step annotate --tools VEP --sample file.vcf.gz --cadd_cache \
    --cadd_InDels /PathToCADD/InDels.tsv.gz \
    --cadd_InDels_tbi /PathToCADD/InDels.tsv.gz.tbi \
    --cadd_WG_SNVs /PathToCADD/whole_genome_SNVs.tsv.gz \
    --cadd_WG_SNVs_tbi /PathToCADD/whole_genome_SNVs.tsv.gz.tbi

Downloading CADD files

An helper script has been designed to help downloading CADD files. Such files are meant to be share between multiple users, so this script is mainly meant for people administrating servers, clusters and advanced users.

nextflow run downloadcache.nf --cadd_cache /Path/To/CADDcache --cadd_version <CADD version> --genome <GENOME>

Using VEP GeneSplicer plugin

To enable the use of the VEP GeneSplicer plugin:

  • use the --genesplicer flag

Example:

nextflow run nf-core/sarek --step annotate --tools VEP --sample file.vcf.gz --genesplicer