GATK VARIANTFILTRATION¶
Run gatk VariantFiltration.
Example¶
This wrapper can be used in the following way:
rule gatk_filter:
input:
vcf="calls/snvs.vcf",
ref="genome.fasta",
# intervals="targets.bed",
output:
vcf="calls/snvs.filtered.vcf",
log:
"logs/gatk/filter/snvs.log",
params:
filters={"myfilter": "AB < 0.2 || MQ0 > 50"},
extra="", # optional arguments, see GATK docs
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"v1.12.2/bio/gatk/variantfiltration"
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://software.broadinstitute.org/gatk/documentation/article?id=11050
Software dependencies¶
gatk4=4.2
snakemake-wrapper-utils=0.3
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 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)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
filters = [
"--filter-name {} --filter-expression '{}'".format(name, expr.replace("'", "\\'"))
for name, expr in snakemake.params.filters.items()
]
intervals = snakemake.input.get("intervals", "")
if not intervals:
intervals = snakemake.params.get("intervals", "")
if intervals:
intervals = "--intervals {}".format(intervals)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' VariantFiltration"
" --variant {snakemake.input.vcf}"
" --reference {snakemake.input.ref}"
" {filters}"
" {intervals}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.vcf}"
" {log}"
)