Awesome
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
-
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.
-
External software:
- picard tool. Note that picard requires Java 1.8 installed.
- 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 | Description | |
|---|---|---|
| Tiffany Delhomme* | delhommet@students.iarc.fr | Developer to contact for support |