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🌮A toil tool to merge vcfs from different callers.
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README.md

toil_mergevcfs

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A toil tool to merge vcfs from different callers.

toil_mergevcfs

Usage

This package uses docker to manage its dependencies, there are 2 ways of using it:

  1. Running the container in single machine mode without --batchSystem support:

     # using docker
     docker run -it papaemmelab/toil_mergevcfs --help
    
     # using singularity
     singularity run docker://papaemmelab/toil_mergevcfs --help
    
  2. 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} \
         --snv
    
     # 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} \
         --snv
    

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
--out Path to the output file
--reference Path to the reference fasta used to left-align indels
--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)

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.

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