iarcbioinfo/vcf_normalization-nf repository overview

⁠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

⁠Parameters

• ⁠Mandatory

• ⁠Optional

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

• ⁠Flags

Flags are special parameters without value.

⁠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

⁠Contributions