ANNOTATION.md

Annotation

Tools

Within Sarek, annotation is done using snpEff, VEP, or 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 then VEP

Using containers

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

Using 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 annotate.nf --tools snpEff --annotateVCF file.vcf.gz --genome GRCh38 --snpEff_cache /Path/To/snpEffCache --annotation_cache
nextflow run annotate.nf --tools VEP --annotateVCF file.vcf.gz --genome GRCh38 --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 annotate.nf --tools VEP --annotateVCF file.vcf.gz --genome GRCh38 --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 build.nf --cadd_cache /Path/To/CADDcache --genome <GENOME>

Using VEP GeneSplicer plugin

To enable the use of the VEP GeneSplicer plugin:

• use the --genesplicer flag

Example:

nextflow run annotate.nf --tools VEP --annotateVCF file.vcf.gz --genome GRCh38 --genesplicer