SNPEFF¶
Annotate predicted effect of nucleotide changes with SnpEff
URL:
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"
# 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_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=4096
wrapper:
"v1.3.1/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.
Software dependencies¶
snpeff==4.3.1t
bcftools=1.11
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 os import path
import shutil
import tempfile
from pathlib import Path
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
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)
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 {java_opts} -dataDir {data_dir} "
"{stats_opt} {csvstats_opt} {extra} "
"{reference} {incalls} "
"{outprefix} > {outcalls} {log}"
)