GATK3 REALIGNERTARGETCREATOR¶
Run gatk3 RealignerTargetCreator
Example¶
This wrapper can be used in the following way:
rule realignertargetcreator:
input:
bam="mapped/{sample}.bam",
ref="genome.fasta",
known="dbsnp.vcf.gz",
output:
intervals="{sample}.intervals",
java_temp=temp(directory("gatk3_indelrealigner/{sample}")),
log:
"logs/gatk/realignertargetcreator/{sample}.log",
params:
extra="", # optional
resources:
mem_mb=1024,
threads: 16
wrapper:
"bio/gatk3/realignertargetcreator"
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” (memory is automatically inferred from resources and temp dir from output.java_temp.
- The extra param allows for additional program arguments.
- For more information see, https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-tutorials/(howto)_Perform_local_realignment_around_indels.md
- Gatk3.jar is not included in the bioconda package, i.e it need to be added to the conda environment manually.
Software dependencies¶
gatk==3.8
snakemake-wrapper-utils==0.1.3
Input/Output¶
Input:
- bam file
- reference genome
- bed file (optional)
- vcf files known variation (optional)
Output:
- target intervals
- temp dir (optional)
Authors¶
- Patrik Smeds
- Filipe G. Vieira
Code¶
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com.com"
__license__ = "MIT"
import os
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)
bed = snakemake.input.get("bed", "")
if bed:
bed = "-L " + bed
known = snakemake.input.get("known", "")
if known:
if isinstance(known, str):
known = "-known {}".format(known)
else:
known = list(map("-known {}".format, known))
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk3 {java_opts} -T RealignerTargetCreator"
" -nt {snakemake.threads}"
" {extra}"
" -I {snakemake.input.bam}"
" -R {snakemake.input.ref}"
" {known}"
" {bed}"
" -o {snakemake.output.intervals}"
" {log}"
)