GATK3 INDELREALIGNER#
Run gatk3 IndelRealigner
Example#
This wrapper can be used in the following way:
rule indelrealigner:
input:
bam="{sample}.bam",
bai="{sample}.bai",
ref="genome.fasta",
fai="genome.fasta.fai",
dict="genome.dict",
known="dbsnp.vcf.gz",
known_idx="dbsnp.vcf.gz.tbi",
target_intervals="{sample}.intervals",
output:
bam="{sample}.realigned.bam",
bai="{sample}.realigned.bai",
log:
"logs/gatk3/indelrealigner/{sample}.log",
params:
extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar", # optional
threads: 16
resources:
mem_mb=1024,
wrapper:
"v3.0.2/bio/gatk3/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
python=3.12.0
snakemake-wrapper-utils=0.6.2
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)
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", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
java_opts = get_java_opts(snakemake)
bed = snakemake.input.get("bed", "")
if bed:
bed = f"--intervals {bed}"
known = snakemake.input.get("known", "")
if known:
if isinstance(known, str):
known = f"--knownAlleles {known}"
else:
known = list(map("----knownAlleles {}".format, known))
output_bai = snakemake.output.get("bai", None)
if output_bai is None:
extra += " --disable_bam_indexing"
shell(
"gatk3 {java_opts}"
" --analysis_type IndelRealigner"
" --input_file {snakemake.input.bam}"
" --reference_sequence {snakemake.input.ref}"
" {known}"
" {bed}"
" --targetIntervals {snakemake.input.target_intervals}"
" {extra}"
" --out {snakemake.output.bam}"
" {log}"
)