GATK VARIANTRECALIBRATOR¶
Run gatk VariantRecalibrator.
Software dependencies¶
- gatk4 ==4.1.4.1
Example¶
This wrapper can be used in the following way:
from snakemake.remote import GS
# GATK resource bundle files can be either directly obtained from google storage (like here), or
# from FTP. You can also use local files.
GS = GS.RemoteProvider()
def gatk_bundle(f):
return GS.remote("genomics-public-data/resources/broad/hg38/v0/{}".format(f))
rule haplotype_caller:
input:
vcf="calls/all.vcf",
ref="genome.fasta",
# resources have to be given as named input files
hapmap=gatk_bundle("hapmap_3.3.hg38.sites.vcf.gz"),
omni=gatk_bundle("1000G_omni2.5.hg38.sites.vcf.gz"),
g1k=gatk_bundle("1000G_phase1.snps.high_confidence.hg38.vcf.gz"),
dbsnp=gatk_bundle("Homo_sapiens_assembly38.dbsnp138.vcf.gz"),
# use aux to e.g. download other necessary file
aux=[gatk_bundle("hapmap_3.3.hg38.sites.vcf.gz.tbi"),
gatk_bundle("1000G_omni2.5.hg38.sites.vcf.gz.tbi"),
gatk_bundle("1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi"),
gatk_bundle("Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi")]
output:
vcf="calls/all.recal.vcf",
tranches="calls/all.tranches"
log:
"logs/gatk/variantrecalibrator.log"
params:
mode="SNP", # set mode, must be either SNP, INDEL or BOTH
# resource parameter definition. Key must match named input files from above.
resources={"hapmap": {"known": False, "training": True, "truth": True, "prior": 15.0},
"omni": {"known": False, "training": True, "truth": False, "prior": 12.0},
"g1k": {"known": False, "training": True, "truth": False, "prior": 10.0},
"dbsnp": {"known": True, "training": False, "truth": False, "prior": 2.0}},
annotation=["QD", "FisherStrand"], # which fields to use with -an (see VariantRecalibrator docs)
extra="", # optional
java_opts="", # optional
wrapper:
"0.59.0/bio/gatk/haplotypecaller"
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.
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
- The extra param alllows for additional program arguments.
- For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050
Authors¶
- Johannes Köster
- Jake VanCampen
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
import os
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")
def fmt_res(resname, resparams):
fmt_bool = lambda b: str(b).lower()
try:
f = snakemake.input.get(resname)
except KeyError:
raise RuntimeError(
"There must be a named input file for every resource (missing: {})".format(
resname
)
)
return "{},known={},training={},truth={},prior={}:{}".format(
resname,
fmt_bool(resparams["known"]),
fmt_bool(resparams["training"]),
fmt_bool(resparams["truth"]),
resparams["prior"],
f,
)
resources = [
"--resource {}".format(fmt_res(resname, resparams))
for resname, resparams in snakemake.params["resources"].items()
]
annotation = list(map("-an {}".format, snakemake.params.annotation))
tranches = ""
if snakemake.output.tranches:
tranches = "--tranches-file " + snakemake.output.tranches
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' VariantRecalibrator {extra} {resources} "
"-R {snakemake.input.ref} -V {snakemake.input.vcf} "
"-mode {snakemake.params.mode} "
"--output {snakemake.output.vcf} "
"{tranches} {annotation} {log}"
)