GATK3 INDELREALIGNER¶
Run gatk3 IndelRealigner
Example¶
This wrapper can be used in the following way:
rule indelrealigner:
input:
bam="mapped/{sample}.bam",
bai="mapped/{sample}.bai",
ref="genome.fasta",
known="dbsnp.vcf.gz",
known_idx="dbsnp.vcf.gz.tbi",
target_intervals="{sample}.intervals"
output:
bam="realigned/{sample}.bam",
bai="realigned/{sample}.bai",
java_temp=temp(directory("/tmp/gatk3_indelrealigner/{sample}")),
log:
"logs/gatk3/indelrealigner/{sample}.log"
params:
extra="" # optional
threads: 16
resources:
mem_mb = 1024
wrapper:
"bio/gatk/indelrealigner"
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
- target intervals to realign
- bed file (optional)
- vcf files known variation (optional)
Output:
- indel realigned bam file
- indel realigned bai file (optional)
- 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))
output_bai = snakemake.output.get("bai", None)
if output_bai is None:
extra += " --disable_bam_indexing"
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk3 {java_opts} -T IndelRealigner"
" {extra}"
" -I {snakemake.input.bam}"
" -R {snakemake.input.ref}"
" {known}"
" {bed}"
" --targetIntervals {snakemake.input.target_intervals}"
" -o {snakemake.output.bam}"
" {log}"
)