vcf_normalization-nf

Nextflow pipeline for vcf normalization

Description

Apply bcftools norm to decompose and normalize variants from a set of VCF (compressed with gzip/bgzip).

This scripts takes a set of a folder containing compressed VCF files (*.vcf.gz) as an input. It consists at four piped steps:

• (optional) filtering of variants (bcftoolvs view -f)
• split multiallelic sites into biallelic records (bcftools norm -m -) and left-alignment and normalization (-f ref)
• sorting (bcftools sort )
• duplicate removal (bcftools norm -d exact) and compression (-Oz)

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:

• bcftools

Caution: bcftools has to be in your $PATH. Try each of the commands bcftools and bgzip, if it returns the options this is ok.

Input

Name	Description
--vcf_folder	Folder containing tumor zipped VCF files

Parameters

• Mandatory

Name	Example value	Description
--ref	/path/to/ref.fasta	Reference fasta file indexed

• Optional

Name	Default value	Description
--output_folder	normalized_VCF/	Folder to output resulting compressed vcf
--filter_opt	-f PASS	Options for bcftools view
--cpu	2	Number of cpus to use
--mem	8	Size of memory used for mapping (in GB)

Note that the default is to filter variants with the PASS flag. To deactivate, use --filter_opt " ".

• Flags

Flags are special parameters without value.

Name	Description
--help	Display help

Usage

Simple use case example:

nextflow run iarcbioinfo/vcf_normalization-nf -r v1.1 -profile singularity --vcf_folder VCF/ --ref ref.fasta

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

Type	Description
VCF.gz, VCF.gz.tbi	Compressed normalized VCF files with indexes

Contributions

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