PICARD MERGEVCFS

Merge vcf files using picard tools.

Software dependencies

  • picard ==2.22.1

Example

This wrapper can be used in the following way:

rule merge_vcfs:
    input:
        vcfs=["snvs.chr1.vcf", "snvs.chr2.vcf"]
    output:
        "snvs.vcf"
    log:
        "logs/picard/mergevcfs.log"
    params:
        extra=""
    wrapper:
        "0.50.4/bio/picard/mergevcfs"

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

"""Snakemake wrapper for picard MergeSamFiles."""

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


from snakemake.shell import shell


inputs = " ".join("INPUT={}".format(f) for f in snakemake.input.vcfs)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")

shell(
    "picard"
    " MergeVcfs"
    " {extra}"
    " {inputs}"
    " OUTPUT={snakemake.output[0]}"
    " {log}"
)