VG CONSTRUCT

Construct variation graphs from a reference and variant calls.

Example

This wrapper can be used in the following way:

rule construct:
    input:
        ref="c.fa",
        vcfgz="c.vcf.gz"
    output:
        vg="graph/c.vg"
    params:
        "--node-max 10"
    log:
        "logs/vg/construct/c.log"
    threads:
        4
    wrapper:
        "v3.8.0/bio/vg/construct"

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.

Software dependencies

• vg=1.56.0

Authors

• Ali Ghaffaari

Code

__author__ = "Ali Ghaffaari"
__copyright__ = "Copyright 2017, Ali Ghaffaari"
__email__ = "ghaffari@mpi-inf.mpg.de"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False)

shell(
    "(vg construct {snakemake.params} --reference {snakemake.input.ref}"
    " --vcf {snakemake.input.vcfgz} --threads {snakemake.threads}"
    " > {snakemake.output.vg}) {log}"
)