svsomaticcns-nf

Consensus calling of Somatic Structural variants from Paired WGS

Description

Pipeline using multiple SV callers for consensus structural variant calling from tumor/normal sequencing data.

Usage

# Run the whole pipeline and consensus of calls
nextflow run iarcbioinfo/sv_somatic_cns-nf -r v1.0 \
-profile singularity  --tn_file tn_pairs..txt \
--input_folder $PWD/CRAM \
--ref hs38DH.fa \
--all_sv_cns \
--output_folder results

#Run Delly and manta only
nextflow run iarcbioinfo/sv_somatic_cns-nf -r v1.0 \
-profile singularity  --tn_file tn_pairs..txt \
--input_folder $PWD/CRAM \
--ref hs38DH.fa \
--delly \
--manta \
--output_folder results_delly_manta

Dependencies

1. 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.
2. External software:
   • DELLY v0.8.7
   • SVABA v1.1.0
   • MANTA v1.6.0
   • SURVIVOR v1.0.7
   • BCFTOOLS v1.10
   • SAMTOOLS v1.10

You can avoid installing all the external software by only installing Docker or singularity. See the IARC-nf repository for more information.

Input (mandatory)

Type	Description
--input_folder	Folder containing all BAM/CRAM files
--tn_file	File containing the list of names of BAM files to be processed
--ref	Fasta file of reference genome [hg38.fa], should be indexed [hg38.fa.fai]
--gtf	GTF file with gene/transcripts/exon annotations [hg38.gtf]
Flags to run each SV caller combinations
--delly	run the Delly SV caller
--manta	run the Manta SV caller
--svaba	run the SVaba SV caller
Short-cut to enable all sv callers plus consensus with survivor
--all_sv_cns	run Delly, Manta, SVaba and integration with SURVIVOR

Example of Tumor/Normal pairs file (--tn_file)

A text file tabular separated, with the following header:

sampleID	tumor	normal
sample1_T1	sample1_T.cram	sample1_N.cram
sample2_T1	sample2_T.cram	sample2_N.cram
sample3_T1	sample3_T.cram	sample3_N.cram

Optional parameters

Name	type	Description
--bam	[flag]	active bam mode [def:cram]
--output_folder	[string]	name of output folder
--cpu	[Integer]	Number of CPUs[def:2]
--mem	[Integer]	Max memory [def:16Gb]

Output

results
├── DELLY                               # DELLY result directory
│   ├── ...
├── SVABA                               # SVABA result directory
│   ├── ...
├── MANTA                               # MANTA result directory
│   ├── ...
├── SURVIVOR                            # SURVIVOR result directory
│   ├── ...
├── nf-pipeline_info                   # NEXTFLOW logs

Limitations

The current version of the pipeline can handle Tumor/Normal pairs only but not multi-region WGS data.

Common errors

Singularity

The first time that the container is built from the docker image, the TMPDIR should be defined in a non parallel file-system, you can set this like:

export TMPDIR=/tmp

Contributions

Name	Email	Description
Matthieu Foll*	follm@iarc.fr	Developer to contact for support (link to specific gitter chatroom)
Alex Di Genova	digenovaa@fellows.iarc.fr	Developer