Awesome
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
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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.
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External software:
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
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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.
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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 | Description | |
|---|---|---|
| Nicolas Alcala* | alcalan@iarc.fr | Developer to contact for support |
| Tiffany Delhomme | delhommet@students.iarc.fr | Developer |