BCFTOOLS CONCAT

Concatenate vcf/bcf files with bcftools.

Software dependencies

  • bcftools ==1.6

Example

This wrapper can be used in the following way:

rule bcftools_concat:
    input:
        calls=["a.bcf", "b.bcf"]
    output:
        "all.bcf"
    params:
        ""  # optional parameters for bcftools concat (except -o)
    wrapper:
        "0.21.0/bio/bcftools/concat"

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Authors

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools concat {snakemake.params} -o {snakemake.output[0]} "
    "{snakemake.input.calls}")