toil_cvflag
A toil implementation of caveman flagging for vcf files.
Usage
This package uses docker to manage its dependencies, there are 2 ways of using it:
-
Running the container in single machine mode without
--batchSystemsupport:# using docker docker run -it papaemmelab/toil_cvflag --help # using singularity singularity run docker://papaemmelab/toil_cvflag --help -
Installing the python package from pypi and passing the container as a flag:
# install package pip install toil_cvflag # run with docker toil_cvflag [TOIL-OPTIONS] [PIPELINE-OPTIONS] --docker papaemmelab/toil_cvflag --volumes <local path> <container path> --batchSystem LSF # run with singularity toil_cvflag [TOIL-OPTIONS] [PIPELINE-OPTIONS] --singularity docker://papaemmelab/toil_cvflag --volumes <local path> <container path> --batchSystem LSF
See docker2singularity if you want to use a singularity image instead of using the docker:// prefix.
Options
The following options are required to run caveman postprocessing:
| Option | Description |
|---|---|
| --vcf | Path to input vcf file |
| --out | Path to caveman flagged output vcf file |
| --normal-bam | Path to normal bam |
| --tumor-bam | Path to tumor bam |
| --bedFileLoc | Path to a folder containing centromeric, snp, hi seq depth, simple repeat bed files |
| --indelBed | A bed file containing germline indels to filter on |
| --unmatchedVCFLoc | Path to folder containing unmatched VCF PON |
| --annoBedLoc | Path to bed files containing annotatable regions and coding regions |
| --sequencing-method | WGS or TGD |
| --bin-size | Number of variants to split the vcf to parallelize flagging (default: 100000) |
Contributing
Contributions are welcome, and they are greatly appreciated, check our contributing guidelines!
Credits
This package was created using Cookiecutter and the papaemmelab/cookiecutter-toil project template.
