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:
"0.59.1/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.
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}"
)