toil_mergevcfs
A toil tool to merge vcfs from different callers.
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_mergevcfs --help # using singularity singularity run docker://papaemmelab/toil_mergevcfs --help -
Installing the python package from pypi and passing the container as a flag:
# install package pip install toil_mergevcfs # run with docker toil_mergevcfs [TOIL-OPTIONS] [PIPELINE-OPTIONS] --docker papaemmelab/toil_mergevcfs --volumes <local path> <container path> --batchSystem LSF \ --vcf {path to vcf1} \ --vcf {path to vcf2} \ --vcf {path to vcf3} \ --out {path to merged output vcf.gz} # run with singularity toil_mergevcfs [TOIL-OPTIONS] [PIPELINE-OPTIONS] --singularity docker://papaemmelab/toil_mergevcfs --volumes <local path> <container path> --batchSystem LSF \ --vcf {path to vcf1} \ --vcf {path to vcf2} \ --vcf {path to vcf3} \ --out {path to merged output vcf.gz}
See docker2singularity if you want to use a singularity image instead of using the docker:// prefix.
Options
| Option | Description |
|---|---|
| --vcf * | Path to a input vcf file. More than one --vcf is required. |
| --out * | Path to the output file |
| --reference | Path to the reference fasta used to left-align indels |
| --tumor-name | Tumor Sample Name to add to output vcf as header |
| --normal-name | Normal Sample Name to add to output vcf as header |
| --bedfile | Bed file to subset the files before merging |
| --threads | Number of extra output compression threads. (default 4) |
| --use-contigs | Merge by vcfs contigs. By default it merges by chromosomes 1-22, X, Y |
| --pass | Flag to filter PASS variants by any caller. |
| --any2lcc | Flag to filter out variants not called by 2 or more callers, and indels by low context complexity (LCC) score. |
| --drivers | Bed files to filter the files after merging |
| --runtime | Runtime minutes for system jobs. (default 90) |
| --memory | Memory for system jobs. (default 4G) |
* Required fields
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.
