SNPEFF

Annotate predicted effect of nucleotide changes with SnpEff

Software dependencies

• snpeff ==4.3.1t
• bcftools =1.10

Example

This wrapper can be used in the following way:

rule snpeff:
    input:
        calls="{sample}.vcf", # (vcf, bcf, or vcf.gz)
        db="resources/snpeff/ebola_zaire" # path to reference db downloaded with the snpeff download wrapper
    output:
        calls="snpeff/{sample}.vcf",   # annotated calls (vcf, bcf, or vcf.gz)
        stats="snpeff/{sample}.html",  # summary statistics (in HTML), optional
        csvstats="snpeff/{sample}.csv" # summary statistics in CSV, optional
    log:
        "logs/snpeff/{sample}.log"
    params:
        extra="-Xmx4g"           # optional parameters (e.g., max memory 4g)
    wrapper:
        "0.56.0/bio/snpeff/annotate"

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
from pathlib import Path

outcalls = snakemake.output.calls
if outcalls.endswith(".vcf.gz"):
    outprefix = "| bcftools view -Oz"
elif outcalls.endswith(".bcf"):
    outprefix = "| bcftools view -Ob"
else:
    outprefix = ""

incalls = snakemake.input[0]
if incalls.endswith(".bcf"):
    incalls = "< <(bcftools view {})".format(incalls)

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

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

data_dir = Path(snakemake.input.db).parent.resolve()

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)

reference = path.basename(snakemake.input.db)

shell(
    "snpEff -dataDir {data_dir} {stats_opt} {csvstats_opt} {extra} "
    "{reference} {incalls} "
    "{outprefix} > {outcalls} {log}"
)