BCFTOOLS VIEW

View vcf/bcf file in a different format.

Software dependencies

  • bcftools ==1.5

Example

This wrapper can be used in the following way:

rule bcf_to_vcf:
    input:
        "{prefix}.bcf"
    output:
        "{prefix}.vcf"
    params:
        ""  # optional parameters for bcftools view (except -o)
    wrapper:
        "0.19.1/bio/bcftools/view"

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 view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")