svaba-nf

September 1, 2020 · View on GitHub

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

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