V-Catherine/mutspec_annot

Annotate VCF files with Annovar

mutspec_annot-nf

mutspec_annot pipeline with Nextflow

Dependencies

1. Install R and libraries

   conda install -c r r
   R
   install.packages(c("data.table","vcfR"))
   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

Execution

nextflow run iarcbioinfo/mutspec-annot.nf --input vcf_folder/ --annovarDBlist Dblist.txt --annovarDBpath /data/annnovar/hg38db/

Options

OPTIONS	TYPE	Description
--input	FOLDER	Folder containing vcf to process
--annovarDBlist	FILE	File with two columns : protocols and operations (see example below)
--extention	TXT	input files extension
--annovarDBpath	PATH	Path to annovarDB
--annovarBinPath	PATH	Path to table_annovar.pl
--thread	INT	Number of thread for table_annovar.pl
--vaf		Add columns with VAF and coverage
--caller	TXT	when using --vaf, indicate the caller (strelka2, mutect2 or haplotypecaller)

Help section

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

nextflow run iarcbioinfo/mutspec_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. Plus you need to add int the same folder the fasta of your genome for the 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/'
                }
        }