GATK GENOTYPEGVCFS¶
Run gatk GenotypeGVCFs.
URL:
Example¶
This wrapper can be used in the following way:
rule genotype_gvcfs:
input:
gvcf="calls/all.g.vcf", # combined gvcf over multiple samples
# N.B. gvcf or genomicsdb must be specified
# in the latter case, this is a GenomicsDB data store
ref="genome.fasta"
output:
vcf="calls/all.vcf",
log:
"logs/gatk/genotypegvcfs.log"
params:
extra="", # optional
java_opts="", # optional
resources:
mem_mb=1024
wrapper:
"v1.1.0/bio/gatk/genotypegvcfs"
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¶
gatk4=4.2
snakemake-wrapper-utils==0.1.3
Input/Output¶
Input:
- GVCF files or GenomicsDB workspace
- reference genome
Output:
- VCF file with genotypes
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. -XX:ParallelGCThreads=10 (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The extra param allows for additional program arguments.
- For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/4405451397659-GenotypeGVCFs
Authors¶
- Johannes Köster
- Jake VanCampen
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
import os
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
interval_file = snakemake.input.get("interval_file", "")
if interval_file:
interval_file = "-L {}".format(interval_file)
dbsnp = snakemake.input.get("known", "")
if dbsnp:
dbsnp = "-D {}".format(dbsnp)
# Allow for either an input gvcf or GenomicsDB
gvcf = snakemake.input.get("gvcf", "")
genomicsdb = snakemake.input.get("genomicsdb", "")
if gvcf:
if genomicsdb:
raise Exception("Only input.gvcf or input.genomicsdb expected, got both.")
input_string = gvcf
else:
if genomicsdb:
input_string = "gendb://{}".format(genomicsdb)
else:
raise Exception("Expected input.gvcf or input.genomicsdb.")
tmpdir = tempfile.gettempdir()
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' GenotypeGVCFs {extra} "
"-V {input_string} "
"-R {snakemake.input.ref} "
"{dbsnp} "
"{interval_file} "
"--tmp-dir {tmpdir} "
"-O {snakemake.output.vcf} {log}"
)