JANNOVAR¶
Annotate predicted effect of nucleotide changes with Jannovar
Software dependencies¶
- jannovar-cli ==0.25
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"
params:
database="hg19_small.ser", # path to jannovar reference dataset
extra="--show-all" # optional parameters
wrapper:
"0.32.0/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.
Authors¶
- Bradford Powell
Code¶
__author__ = "Bradford Powell"
__copyright__ = "Copyright 2018, Bradford Powell"
__email__ = "bpow@unc.edu"
__license__ = "BSD"
from snakemake.shell import shell
shell.executable("bash")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
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} {log}")