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https://github.com/nci-gdc/somaticsniper-cwl
CWL for GDC SomaticSniper
https://github.com/nci-gdc/somaticsniper-cwl
bioinformatics cwl workflow
Last synced: 6 days ago
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CWL for GDC SomaticSniper
- Host: GitHub
- URL: https://github.com/nci-gdc/somaticsniper-cwl
- Owner: NCI-GDC
- License: apache-2.0
- Created: 2016-01-28T22:49:06.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2021-03-25T15:58:23.000Z (almost 4 years ago)
- Last Synced: 2024-04-14T12:44:40.683Z (9 months ago)
- Topics: bioinformatics, cwl, workflow
- Language: Common Workflow Language
- Homepage:
- Size: 119 KB
- Stars: 0
- Watchers: 10
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# GDC SomaticSniper CWL
The purpose of SomaticSniper is to identify single nucleotide positions that are different between tumor and normal. It takes a tumor bam and a normal bam and compares the two to determine the differences.
Original SomaticSniper: http://gmt.genome.wustl.edu/packages/somatic-sniper/index.html
## Docker
All the docker images are built from `Dockerfile`s at https://github.com/NCI-GDC/somaticsniper-tool.
## CWL
https://www.commonwl.org/
The CWL are tested under multiple `cwltools` environments. The most tested one is:
* cwltool 1.0.20180306163216
## For external users
The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in [GDC reference files](https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files "GDC reference files"). For any questions related to GDC data, please contact the GDC Help Desk at [email protected].
There is a production-ready GDC CWL workflow at https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow, which uses this repo as a git submodule.
Please notice that you may want to change the docker image host of `dockerPull:` for each CWL.
To use CWL directly from this repo, we recommend to run
* `tools/multi_somaticsniper.cwl` on an array of tumor/normal mpileup files.
To run CWL:
```
>>>>>>>>>>Multi SomaticSniper<<<<<<<<<<
cwltool tools/multi_somaticsniper.cwl -h
/home/ubuntu/.virtualenvs/p2/bin/cwltool 1.0.20180306163216
Resolved 'tools/multi_somaticsniper.cwl' to 'file:///mnt/SCRATCH/githubs/submodules/s/somaticsniper-cwl/tools/multi_somaticsniper.cwl'
usage: tools/multi_somaticsniper.cwl [-h] [--base_q BASE_Q] [--fout FOUT]
[--gor] [--loh] [--map_q MAP_Q] --mpileup
MPILEUP [--nhap NHAP] --normal_input
NORMAL_INPUT [--pd PD] --ppa [--pps PPS]
--psc --reference REFERENCE
[--theta THETA] --thread_count
THREAD_COUNT --tumor_input TUMOR_INPUT
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--base_q BASE_Q filtering somatic snv output with somatic quality less
than this value
--fout FOUT output format (classic/vcf/bed)
--gor do not report Gain of Reference variants as determined
by genotypes (T/F)
--loh do not report LOH variants as determined by genotypes
(T/F)
--map_q MAP_Q filtering reads with mapping quality less than this
value
--mpileup MPILEUP mpileup file on t/n pair
--nhap NHAP number of haplotypes in the sample
--normal_input NORMAL_INPUT
--pd PD prior of a difference between two haplotypes
--ppa Use prior probabilities accounting for the somatic
mutation rate (T/F)
--pps PPS prior probability of a somatic mutation (implies -J)
--psc disable priors in the somatic calculation. Increases
sensitivity for solid tumors (T/F)
--reference REFERENCE
human reference genome
--theta THETA theta in maq consensus calling model (for -c/-g)
--thread_count THREAD_COUNT
--tumor_input TUMOR_INPUT
```
## For GDC users
See https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow.