digenoma-lab / strelka2-nf

strelka2-nf

Strelka v2 pipeline with Nextflow

Dependencies

1. Nextflow : for common installation procedures see the IARC-nf repository.
2. Install Strelka v2.

Input

Type	Description
--input_folder	folder with bam/cram files
--input_file	Tab delimited text file with either two columns called normal and tumor (somatic mode) or one column called bam (germline mode); optionally, a column called sample containing sample names to be used for naming the files can be provided and for genotyping (see genotyping mode below) a column called vcf has to be provided

Note: the file provided to --input_file is where you can define pairs of bam/cram to analyse with strelka in somatic mode. It's a tabular file with 2 columns normal and tumor.

normal	tumor
normal1.cram	tumor2.cram
normal2.cram	tumor2.cram
normal3.cram	tumor3.cram

Parameters

• Mandatory

Name	Example value	Description
--ref	hg19.fasta	genome reference

• Optional

Name	Default value	Description
--mode	somatic	Mode for variant calling; one of somatic, germline, genotyping
--output_folder	strelka_ouptut	Output folder for vcf files
--cpu	2	number of CPUs
--mem	20	memory
--strelka	path inside docker and singularity containers	Strelka installation dir
--config	default conf of strelka	Use custom configuration file
--callRegions	none	Region bed file
--ext	cram	extension of alignment files (bam or cram)

• Flags

Flags are special parameters without value.

Name	Description
--help	print usage and optional parameters
--exome	automatically set up parameters for exome data
--rna	automatically set up parameters for rna data (only available for --mode germline)
--AF	Add AF field to VCF (only available for --mode somatic)
--outputCallableRegions	Create a BED track containing regions which are determined to be callable

Usage

mode somatic

nextflow run iarcbioinfo/strelka2-nf r v1.2a -profile singularity --mode somatic --ref hg38.fa --tn_pairs pairs.txt --input_folder path/to/cram/ --strelka path/to/strelka/

To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

mode germline

nextflow run iarcbioinfo/strelka2-nf r v1.2a -profile singularity --mode germline --ref hg38.fa --input_folder path/to/cram/ --strelka path/to/strelka/

genotyping

When using the input_file mode, if a vcf column with the path to a VCF file for each sample containing a list of somatic variant is provided, the pipeline will use the --forcedGT option from strelka that genotypes these positions, and compute a bedfile for these positions so only variants from the VCF will be genotyped. Note that genotyping can be performed both in somatic mode (in which case tumor/normal pairs must be provided) and germline mode (in which case a single cram file must be provided).

Output

Type	Description
VCFs/raw/*.vcf.gz	VCF files before filtering
VCFs/withAF/*.vcf	VCF files with AF field (optional, requires flag --AF)
VCFs/filtered/*PASS.vcf.gz	final compressed and indexed VCF files (optionally with flag --AF)
CallableRegions/*.bed.gz	compressed and indexed BED files (optionally with flag --outputCallableRegions)

Final vcf files have companion tabix index files (.tbi). Note that in germline mode, the VCF outputted corresponds to variants only (file variants.vcf.gz from strelka).

Directed Acyclic Graph

Contributions

Name	Email	Description
Vincent Cahais	[e-mail]	Developer
Nicolas Alcala	[e-mail]	Developer