GATK GENOTYPEGVCFS¶
Run gatk GenotypeGVCFs.
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:
"v1.19.1/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.
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
Software dependencies¶
gatk4=4.2
snakemake-wrapper-utils=0.5
Input/Output¶
Input:
- GVCF files or GenomicsDB workspace
- reference genome
Output:
- VCF file with genotypes
Authors¶
- Johannes Köster
- Jake VanCampen
- Filipe G. Vieira
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)
intervals = snakemake.input.get("intervals", "")
if not intervals:
intervals = snakemake.params.get("intervals", "")
if intervals:
intervals = "--intervals {}".format(intervals)
dbsnp = snakemake.input.get("known", "")
if dbsnp:
dbsnp = "--dbsnp {}".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.")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' GenotypeGVCFs"
" --variant {input_string}"
" --reference {snakemake.input.ref}"
" {dbsnp}"
" {intervals}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.vcf}"
" {log}"
)