LiftOver-nf

Nextflow pipeline to convert BED/VCF files between two genomes

Description

Use picard tool to lift over BED or VCF files.

This scripts takes a set of a folder containing VCF or BED files as an input.

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:

• picard tool. Note that picard requires Java 1.8 installed.

3. External files:

• The pipeline needs chains files, which contain all the information about translation between two genomes. They can be downloaded from the UCSC website selecting the genome you want to translate from.

Input

Name	Description
--input_folder	Folder containing BED or VCF files
--chain_folder	Folder containing chain files
--ref	Reference fasta file for the target genome

If input is a VCF folder, files may have .vcf or .vcf.gz extension. If input is a BED folder, files may have .bed or .txt extension.

Parameters

• Mandatory

Name	Example value	Description
--genome_from	Genome you want to translate from
--genome_into	Genome you want to translate into

Examples of accepted values for --genome_from and --genome_into parameter:

• hg38 / hg19 / hg18 / hg17

• GRCh38 / GRCh37

• Optional

Name	Default value	Description
--output_folder	liftover_output/	Folder to output resulting translated files

• Flags

Flags are special parameters without value.

Name	Description
--help	Display help

Usage

Simple use case example:

nextflow run iarcbioinfo/LiftOver-nf --input_folder VCF/ --ref ref.fasta

Output

Type	Description
BED/VCF	Translated BED/VCF files

Contributions

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