iarcbioinfo/table_annovar-nf repository overview

⁠table_annovar-nf

⁠Nextflow pipeline to annotate variant files with annovar

⁠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

⁠Parameters

• ⁠Optional

The default annovar params are: -remove -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.

⁠Usage

Simple use case example:

nextflow run iarcbioinfo/table_annovar-nf -r v1.0 -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).

⁠Output

See info on output annovar format here⁠.

⁠Contributions