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table_annovar-nf

Nextflow pipeline to annotate variant files with annovar

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Workflow representation

Description

This pipeline runs table_annovar.pl on a folder full of vcf files.

Dependencies

  1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.

  2. External software:

  • annovar
  • bcftools, only used if input is in vcf format (option --table_extension vcf or vcf.gz)

Caution: the perl script annotate_variation.pl and bcftools have to be in your $PATH (note: in case you are using the conda, docker, or singularity profiles, bcftools will automatically be in your $PATH but not annotate_variation.pl).

Input

Name Description
--table_folder Folder containing tables to process

Parameters

  • Optional

Name Default value Description
--output_folder . Folder to output resulting compressed vcf
--annovar_params See below Parameters given to table_annovar.pl
--cpu 1 Number of cpus to use
--mem 4 Size of memory used for mapping (in GB)
--annovar_db Annovar_db Folder with annovar databases
--buildver hg38 Version of genome build
--table_extension tsv Extension of input tables

The default annovar params are: --codingarg -includesnp -protocol ensGene, exac03nontcga,esp6500siv2_all,1000g2015aug_all,gnomad211_genome,gnomad211_exome,clinvar_20190305,revel,dbnsfp35a,dbnsfp31a_interpro,intervar_20180118,cosmic84_coding,cosmic84_noncoding,avsnp150,phastConsElements100way,wgRna -operation g,f,f,f,f,f,f,f,f,f,f,f,f,f,r,r -otherinfo, which imply that the corresponding annovar databases are installed. You can specify any other options using the annovar_params option.

  • Flags

Flags are special parameters without value.

Name Description
--help Display help

Usage

Simple use case example:

nextflow run iarcbioinfo/table_annovar-nf -r v1.1 -profile singularity --table_folder VCF/ --table_extension vcf

To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

Note that because due to licensing considerations, annovar has to be installed locally and cannot be included in a container, the path to table_annovar.pl needs to be in the $PATH environment variable and needs to be mounted (e.g., using nextflow option singularity.runOptions = "-B /home/bin" and adding /home/bin to environment variable SINGULARITYENV_APPEND_PATH with nextflow option singularity.envWhitelist="SINGULARITYENV_APPEND_PATH").

Output

Type Description
file_multianno.txt Annovar tables
file_multianno.vcf.gz, file_multianno.vcf.gz.tbi (optional, if --table_extension vcf or vcf.gz) Compressed and indexed annotated VCF files
coding_change/file_coding_change.fa (optional, if exonic variant function is computed) fasta file with altered transcripts

See info on output annovar format here.

Contributions

Name Email Description
Nicolas Alcala* alcalan@iarc.fr Developer to contact for support
Tiffany Delhomme delhommet@students.iarc.fr Developer