Consensus calling of Somatic Structural variants from Paired WGS
Pipeline using multiple SV callers for consensus structural variant calling from tumor/normal sequencing data.
# Run the whole pipeline and consensus of calls
nextflow run iarcbioinfo/sv_somatic_cns -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 -r v1.0 \
-profile singularity --tn_file tn_pairs..txt \
--input_folder $PWD/CRAM \
--ref hs38DH.fa \
--delly \
--manta \
--output_folder results_delly_manta
- 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:
You can avoid installing all the external software by only installing Docker or singularity. See the IARC-nf repository for more information.
| 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] |
| 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 |
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
| 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] |
results
├── DELLY # DELLY result directory
│ ├── ...
├── SVABA # SVABA result directory
│ ├── ...
├── MANTA # MANTA result directory
│ ├── ...
├── SURVIVOR # SURVIVOR result directory
│ ├── ...
├── nf-pipeline_info # NEXTFLOW logs
The current version of the pipeline can handle Tumor/Normal pairs only but not multi-region WGS data.
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
| Name | Description | |
|---|---|---|
| Matthieu Foll* | [email protected] | Developer to contact for support (link to specific gitter chatroom) |
| Alex Di Genova | [email protected] | Developer |