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
        genes="snpeff/{sample}.genes" # summary statistics by gene (TSV), optional
        # if either "genes" or "stats" outputs are provided, both are created
    log:
        "logs/snpeff/{sample}.log"
    params:
        reference="ebola_zaire", # reference name (from `snpeff databases`)
        extra=""                 # optional parameters
    wrapper:
        "0.27.0/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 {dataDir} {statsOpt} {extra}"
                " {snakemake.params.reference} {snakemake.input}"
                " > {snakemake.output.vcf}) {log}")

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

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

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

stats = snakemake.output.get("stats", "")
genes = snakemake.output.get("genes", "")
if stats or genes:
    with tempfile.TemporaryDirectory() as stats_tempdir:
        if not stats:
            if genes.endswith('.genes.txt'):
                stats = genes[:-10] + '.html'
            else:
                stats = genes + '.html'
        if not genes:
            if stats.endswith('.html'):
                genes = stats[:-5] + '.genes.txt'
            else:
                genes = stats + '.genes.txt'
        statsOpt = '-stats "%s"'%path.join(stats_tempdir, 'stats')
        shell(shell_command)
        shutil.move(path.join(stats_tempdir, 'stats'), stats)
        shutil.move(path.join(stats_tempdir, 'stats.genes.txt'), genes)
else:
    statsOpt = '-noStats'
    shell(shell_command)