skeitaa/gama_annot-nf_sk

Annotate VCF files with Annovar

gama_annot-nf

gama_annot pipeline with Nextflow

Annotate vcf files using annovar + additional scripts. Works for Mutect2, Strelka2 and HaplotypeCaller outputs

Dependencies

1. Install R and libraries

   conda install -c r r
   R
   if (!requireNamespace("BiocManager", quietly = TRUE))
   		install.packages("BiocManager")
   BiocManager::install(c("biostrings","getoptlong"))

2. Install annovar.

3. Install nextflow.

   curl -fsSL get.nextflow.io | bash

   And move it to a location in your $PATH (/usr/local/bin for example here):

   sudo mv nextflow /usr/local/bin

4. If the vcf files to annotate are from Strelka2 but were not generated using IARCbioinfo Strelka2 pipeline, first run fixStrelkaOutput.sh. This will add GT field (mandatory for Annovar)

Execution

nextflow run iarcbioinfo/gama_annot-nf --input vcf_folder/ --annovarDBlist Dblist.txt --annovarDBpath /data/annnovar/hg38db/ --pass PASS --context --caller strelka2 --extention vcf.gz

nextflow run iarcbioinfo/gama_annot-nf --input vcf_folder/ --annovarDBlist Dblist.txt --annovarDBpath /data/annnovar/hg38db/ --pass PASS,clustered_events --context --caller mutect2 --extention vcf

Options

OPTIONS	TYPE	Description
--input	FOLDER	Folder containing vcf to process
--annovarDBlist	FILE	File with two columns : protocols and operations (see example below)
--extension	TXT	input files extension
--annovarDBpath	PATH	Path to annovarDB
--annovarBinPath	PATH	Path to table_annovar.pl
--cpu	INT	Number of used by table_annovar.pl default (8)
--mem	INT	Size of memory used by gama_annot in GB default (64)
--caller	TXT	Add columns with VAF and coverage for corresponding software (strelka2, mutect2 or haplotypecaller)'
--pass	TXT	Value on which the variants should be filtered prior to annotation (default : PASS)
--context	FLAG	Add context, strand and user Annotations

Help section

You can print the help manual by providing --help in the execution command line:

nextflow run iarcbioinfo/gama_annot-nf --help

This shows details about optional and mandatory parameters provided by the user.

annovarDblist .txt format

The annovarDBlist file is where you can define annotations. See example mm10.list in demo folder.

annovarDBpath

The annovarDBpath is where your annovar database is located. This folder is created using the annotate_variation.pl script from annovar. The name of the folder should be genomedb (for example hg38db or mm10db). You also need to add in the same folder the reference of your genome for the context annotation (specific ".fa" file compatible with the specific context annotation)

Global parameters

--annovarBinPath is mandatory parameters but can be defined in your nextflow config file (~/.nextflow/config or config in the working directory) and so not set as inputs.

The following is an example of config part defining this:

profiles {

        standard {
                params {
                   annovarBinPath = '/data/annovar/bin/'
                   annovarDBpath = '/data/annovarDB/hg38db/'
                }
        }