JANNOVAR

Annotate predicted effect of nucleotide changes with `Jannovar<https://doc-openbio.readthedocs.io/projects/jannovar/en/master/>`_

Example

This wrapper can be used in the following way:

rule jannovar:
    input:
        vcf="{sample}.vcf",
        pedigree="pedigree_ar.ped" # optional, contains familial relationships
    output:
        "jannovar/{sample}.vcf.gz"
    log:
        "logs/jannovar/{sample}.log"
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mg}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_gb = 1
    params:
        database="hg19_small.ser", # path to jannovar reference dataset
        extra="--show-all"         # optional parameters
    wrapper:
        "0.72.0/bio/jannovar"

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

  • jannovar-cli==0.31
  • snakemake-wrapper-utils==0.1.3

Authors

  • Bradford Powell

Code

__author__ = "Bradford Powell"
__copyright__ = "Copyright 2018, Bradford Powell"
__email__ = "bpow@unc.edu"
__license__ = "BSD"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

shell.executable("bash")

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

pedigree = snakemake.input.get("pedigree", "")
if pedigree:
    pedigree = '--pedigree-file "%s"' % pedigree

shell(
    "jannovar annotate-vcf --database {snakemake.params.database}"
    " --input-vcf {snakemake.input.vcf} --output-vcf {snakemake.output}"
    " {pedigree} {extra} {java_opts} {log}"
)