GATK HAPLOTYPECALLER¶
Run gatk HaplotypeCaller.
Example¶
This wrapper can be used in the following way:
rule haplotype_caller:
input:
# single or list of bam files
bam="mapped/{sample}.bam",
ref="genome.fasta"
# known="dbsnp.vcf" # optional
output:
gvcf="calls/{sample}.g.vcf",
log:
"logs/gatk/haplotypecaller/{sample}.log"
params:
extra="", # optional
java_opts="", # optional
# optional specification of memory usage of the JVM that snakemake will respect with global
# resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
# and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=1024
wrapper:
"0.68.0/bio/gatk/haplotypecaller"
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.
Software dependencies¶
gatk4==4.1.4.1
snakemake-wrapper-utils==0.1.3
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
- The extra param alllows for additional program arguments.
- For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050
Authors¶
- Johannes Köster
- Jake VanCampen
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
import os
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
known = snakemake.input.get("known", "")
if known:
known = "--dbsnp " + known
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
bams = snakemake.input.bam
if isinstance(bams, str):
bams = [bams]
bams = list(map("-I {}".format, bams))
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' HaplotypeCaller {extra} "
"-R {snakemake.input.ref} {bams} "
"-ERC GVCF "
"-O {snakemake.output.gvcf} {known} {log}"
)