wwliao/somatic_sv_workflow repository overview

⁠Somatic SV Workflow

With modifications for CWL integration

Contact Matt Wyczalkowski ([email protected]⁠) with questions

⁠SV Caller

• Manta 1.4.0
• Filters: Only select the variants which pass the following criteria:
  • Sample site depth is less than 3x the median chromosome depth near one or both variant breakends
  • Somatic score is greater than 30
  • For a small variant (<1000 bases) in the normal sample, the fraction of reads with MAPQ0 around either breakend doesn't exceed 0.4

⁠Run Notes

There are a number of ways to run SomaticSV workflow, as discussed in Development Notes below. The following instructions are for running SomaticSV using Rabix Executor using a simple task manager, developed specifically for CPTAC3 analyses.

⁠Installation

Install Docker⁠ Be sure it is running before running rabix.

Install Rabix Executor⁠

wget https://github.com/rabix/bunny/releases/download/v1.0.5-1/rabix-1.0.5.tar.gz -O rabix-1.0.5.tar.gz && tar -xvf rabix-1.0.5.tar.gz

Test Rabix Executor with,

cd rabix-cli-1.0.5
./rabix examples/dna2protein/dna2protein.cwl.json examples/dna2protein/inputs.json

This should run for a few seconds and then produce output like,

[2018-04-20 14:38:24.655] [INFO] Job root.Translate has completed
{
  "output_protein" : {
    "basename" : "protein.txt",
    "checksum" : "sha1$55adf0ec2ecc6aee57a774d48216ac5a97d6e5ba",
    "class" : "File",
    "contents" : null,
    "dirname" : "/Users/mwyczalk/tmp/tin-daisy/rabix-cli-1.0.5/examples/dna2protein/dna2protein.cwl-2018-04-20-143817.231/root/Translate",
    "format" : null,
    "location" : "file:///Users/mwyczalk/tmp/tin-daisy/rabix-cli-1.0.5/examples/dna2protein/dna2protein.cwl-2018-04-20-143817.231/root/Translate/protein.txt",
    "metadata" : null,
    "nameext" : ".txt",
    "nameroot" : "protein",
    "path" : "/Users/mwyczalk/tmp/tin-daisy/rabix-cli-1.0.5/examples/dna2protein/dna2protein.cwl-2018-04-20-143817.231/root/Translate/protein.txt",
    "secondaryFiles" : [ ],
    "size" : 9
  }
}

Install SomaticSV⁠

git clone https://github.com/mwyczalkowski/somatic_sv_workflow.git

The following packages are also required for the simple task manager:

• jq⁠
• GNU Parallel⁠

⁠Running CPTAC3 analyses

Example of CPTAC3 analyses is in demo/task_call/katmai.C3. Scripts in this directory can be modified in place, or copied and modified in another directory.

⁠1. Edit project_config.sh

The project_config.sh file has all paths and other definitions specific to a given system (e.g., katmai) and project (e.g., GRCh38 CPTAC3 data). In particular, need to specify path to BamMap file and other details described there.

⁠2. Create dat/cases.dat file

This file has list of all case names which will be analyzed as part of this project. Case names (e.g., C3L-00001) must be unique in this file, and must match the case names in the BamMap file.

⁠3. Run 1_make_yaml.sh

This generates a series of YAML files, which provide inputs to Rabix (and Cromwell) CWL workflow managers, one per case. This script also creates file dat/analysis_pre-summary.dat, which is used to report analysis results once they are complete.

⁠4. Run 2_run_tasks.sh

This launches the SomaticSV workflow using Rabix, either one at a time (default) or several at a time using GNU parallel. For the latter, invoke as,

2_run_tasks.sh -J 4

if you wish to run four at a time. The dry run flag (-d) is useful for testing of configuration.

This step will write results to two places specified in project_config.sh: LOGD and RABIXD. Watch LOGD/CASE.err for execution progress

⁠5. Run 3_make_analysis_summary.sh

When analysis completes, this step will create an analysis summary file which reports on the path to the output VCF file per case, and the input files which were used to generate it.

This creates analysis description file like,

# case  disease data    file_format tumor_name  tumor_uuid  normal_name normal_uuid
C3L-00081   LSCC    /diskmnt/Projects/cptac_scratch/Rabix/SomaticSV-2019-03-11-122143.684/root/output/results/variants/final.SV.WGS.vcf VCF C3L-00081.WGS.T.hg38    cb4885fd-11cd-4eca-a876-35c74daf9feb    C3L-00081.WGS.N.hg38    4571e0d7-4c43-4ff8-aad2-f39bc4964cdf
C3L-00104   GBM /diskmnt/Projects/cptac_scratch/Rabix/SomaticSV-2019-03-11-122143.817/root/output/results/variants/final.SV.WGS.vcf VCF C3L-00104.WGS.T.hg38    d1be16bb-3b12-40f2-ac23-99fabddc615a    C3L-00104.WGS.N.hg38    b671161a-35d8-41ec-af05-22e5d61df42a
C3L-00365   GBM /diskmnt/Projects/cptac_scratch/Rabix/SomaticSV-2019-03-11-122143.962/root/output/results/variants/final.SV.WGS.vcf VCF C3L-00365.WGS.T.hg38    0976b529-4cf1-4ce0-9777-5700dc51cede    C3L-00365.WGS.N.hg38    4d6b2cf2-0e59-4d7e-8189-7ce030358a1e
C3L-00415   LSCC    /diskmnt/Projects/cptac_scratch/Rabix/SomaticSV-2019-03-15-183753.761/root/output/results/variants/final.SV.WGS.vcf VCF C3L-00415.WGS.T.hg38    51a9bfe4-562f-44a7-b1c5-e5237c92b927    C3L-00415.WGS.N.hg38    1415f178-da4e-478d-9909-53e201c259e 

Analysis description file details⁠

⁠Development notes

⁠Demo data

For development and testing purposes, we distribute Demo data obtained from Manta distribution⁠ in demo/demo_data directory, consisting of small tumor/normal BAM files and a reference. Prior to testing, need to uncompress the reference with,

tar -xvjf Homo_sapiens_assembly19.COST16011_region.fa.tar.bz2

⁠Demo projects

./demo directory contains example runs with the workflow executed directly (i.e., inside docker container), by calling docker, and by calling CWL (Rabix and Cromwell).