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svaba-nf
Structural variant calling
Description
Perform structural variant calling with SvABA.
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.
- SvABA: see official installation here.
Input
| Type | Description |
|---|---|
| --input_folder | Folder containing normal (.normal.bam) and tumor (.tumor.bam) BAM files |
| --correspondance | A correspondance file, with columns ID, tumor, and normal specifying the name of the sample and the tumor/normal file names in the input folder |
Parameters
-
Mandatory
| Name | Example value | Description |
|---|---|---|
| --ref | ref.fa | Path to reference fasta file. It should be indexed |
-
Optional
| Name | Default value | Description |
|---|---|---|
| --output_folder | "." | Path to output folder |
| --dbsnp_file | dbsnp_indel.vcf | DbSNP file, e.g. available here |
| --cpu | 1 | Number of cpu to use |
| --mem | 4 | Size of memory used in GB |
| --targets | NULL | bed file with target positions |
| --options | NULL | List of options to pass to svaba |
| Name | Description |
|---|---|
| --help | Display help |
Download test data set
git clone https://github.com/iarcbioinfo/data_test
Usage
nextflow run IARCbioinfo/svaba-nf -r v1.0 -profile singularity--input_folder path/to/input/ --svaba path/to/svaba/ --ref_file path/to/ref/ --dbsnp_file path/to/dbsnp_indel.vcf --output_folder /path/to/output
To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker).
Tumor-only mode
To trigger the Tumor-only mode in some samples, put "None" (with capital N) in the normal column of the corresponding sample.
Output
| Name | Description |
|---|---|
| txts (.bps.txt.gz) | Raw, unfiltered variants |
| BAMs (.contigs.bam) | Unsorted assembly contigs as aligned to the reference with BWA-MEM |
| Logs (.log) | Run-time information |
| txts (.discordants.txt.gz) | Discordant reads identified with 2+ reads |
| VCFs (.vcf ) | VCF of rearrangements and indels |
Directed Acyclic Graph
Contributions
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | AlcalaN@iarc.fr | Developer to contact for support |
| Tiffany Delhomme | DelhommeT@students.iarc.fr | Developer |