iarcbioinfo/vt-nf
vt normalization with nextflow
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iarcbioinfo/vt-nf repository overview
vt-nf
Nextflow pipeline for vt normalization
Description
Apply vt 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:
- decomposition of haplotypes (
vt decompose) - decomposition of variant blocks (
vt decompose_blocksub) - normalization with reference (
vt normalize) - compression with bgzip (
bgzip)
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:
- vt
- bgzip and tabix from
samtools/htslib
Caution: vt, tabix and bgzip have to be in your $PATH. Try each of the commands vt, tabix 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 | vt_VCF/ | Folder to output resulting compressed vcf |
-
Flags
Flags are special parameters without value.
| Name | Description |
|---|---|
--help | Display help |
Usage
Simple use case example:
nextflow run iarcbioinfo/vt-nf --vcf_folder VCF/ --ref ref.fasta
Output
| Type | Description |
|---|---|
| VCF | Compressed normalized VCF files |
Contributions
| Name | Description | |
|---|---|---|
| Tiffany Delhomme* | [email protected] | Developer to contact for support |
Tag summary
Content type
Image
Digest
Size
303.5 MB
Last updated
over 7 years ago
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