BCFTOOLS INDEX

Index vcf/bcf file.

Software dependencies

  • bcftools ==1.10

Example

This wrapper can be used in the following way:

rule bcftools_index:
    input:
        "a.bcf"
    output:
        "a.bcf.csi"
    params:
        extra=""  # optional parameters for bcftools index
    wrapper:
        "0.67.0/bio/bcftools/index"

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

  • Jan Forster

Code

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


from snakemake.shell import shell

## Extract arguments
extra = snakemake.params.get("extra", "")

shell("bcftools index" " {extra}" " {snakemake.input[0]}")