ENSEMBL-VARIATION¶
Download known genomic variants from ENSEMBL FTP servers, and store them in a single .vcf.gz file.
Software dependencies¶
- bcftools >=1.10
- curl
Example¶
This wrapper can be used in the following way:
rule get_variation:
output:
vcf="refs/variation.vcf.gz"
# optional: add fai to get VCF with annotated contig lengths (as required by GATK)
# fai="refs/genome.fasta.fai"
params:
species="saccharomyces_cerevisiae",
release="98",
build="R64-1-1",
type="all" # one of "all", "somatic", "structural_variation"
log:
"logs/get_variation.log"
cache: True # save space and time with between workflow caching (see docs)
wrapper:
"0.53.0/bio/reference/ensembl-variation"
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¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
import tempfile
import subprocess
import sys
from snakemake.shell import shell
from snakemake.exceptions import WorkflowError
species = snakemake.params.species.lower()
release = int(snakemake.params.release)
build = snakemake.params.build
type = snakemake.params.type
branch = ""
if release >= 81 and build == "GRCh37":
# use the special grch37 branch for new releases
branch = "grch37/"
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
if type == "all":
if species == "homo_sapiens" and release >= 93:
suffixes = [
"-chr{}".format(chrom) for chrom in list(range(1, 23)) + ["X", "Y", "MT"]
]
else:
suffixes = [""]
elif type == "somatic":
suffixes = ["_somatic"]
elif type == "structural_variations":
suffixes = ["_structural_variations"]
else:
raise ValueError(
"Unsupported type {} (only all, somatic, structural_variations are allowed)".format(
type
)
)
species_filename = species if release >= 91 else species.capitalize()
urls = [
"ftp://ftp.ensembl.org/pub/{branch}release-{release}/variation/vcf/{species}/{species_filename}{suffix}.vcf.gz".format(
release=release,
species=species,
suffix=suffix,
species_filename=species_filename,
branch=branch,
)
for suffix in suffixes
]
download = ("bcftools concat -Oz {urls}" if len(urls) > 1 else "curl -L {urls}").format(
urls=" ".join(urls)
)
try:
if snakemake.input.get("fai"):
# in case of a given .fai, reheader the VCF such that contig lengths are defined
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"({download} > {tmpdir}/out.vcf.gz && "
" bcftools reheader --fai {snakemake.input.fai} {tmpdir}/out.vcf.gz | bcftools view -Oz -o {snakemake.output[0]}) {log}"
)
else:
# without .fai, just concatenate
shell("{download} > {snakemake.output[0]} {log}")
except subprocess.CalledProcessError as e:
if snakemake.log:
sys.stderr = open(snakemake.log[0], "a")
print(
"Unable to download variation data from Ensembl. "
"Did you check that this combination of species, build, and release is actually provided?",
file=sys.stderr,
)
exit(1)