SNPEFF

Annotate predicted effect of nucleotide changes with SnpEff

Software dependencies

  • snpeff ==4.3.1t

Example

This wrapper can be used in the following way:

rule snpeff:
    input:
        "{sample}.vcf",
    output:
        vcf="snpeff/{sample}.vcf",    # the main output file, required
        stats="snpeff/{sample}.html", # summary statistics (in HTML), optional
        csvstats="snpeff/{sample}.csv" # summary statistics in CSV, optional
    log:
        "logs/snpeff/{sample}.log"
    params:
        reference="ebola_zaire", # reference name (from `snpeff databases`)
        extra="-Xmx4g"                 # optional parameters (e.g., max memory 4g)
    wrapper:
        "0.30.0/bio/snpeff"

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
from os import path
import shutil
import tempfile

shell.executable("bash")
shell_command =("(snpEff {data_dir} {stats_opt} {csvstats_opt} {extra}"
                " {snakemake.params.reference} {snakemake.input}"
                " > {snakemake.output.vcf}) {log}")

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

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

data_dir = snakemake.params.get("data_dir", "")
if data_dir:
    data_dir = '-dataDir "%s"'%data_dir

stats = snakemake.output.get("stats", "")
csvstats = snakemake.output.get("csvstats", "")
csvstats_opt = '' if not csvstats else '-csvStats {}'.format(csvstats)
stats_opt = '-noStats' if not stats  else '-stats {}'.format(stats)

shell(shell_command)
    #if stats:
    #    shutil.copy(path.join(stats_tempdir, 'stats'), stats)
    #if genes:
    #    shutil.copy(path.join(stats_tempdir, 'stats.genes.txt'), genes)