GATK SPLITNCIGARREADS¶
Run gatk SplitNCigarReads.
Software dependencies¶
- gatk4 ==4.1.4.1
Example¶
This wrapper can be used in the following way:
rule splitncigarreads:
input:
bam="mapped/{sample}.bam",
ref="genome.fasta"
output:
"split/{sample}.bam"
log:
"logs/gatk/splitNCIGARreads/{sample}.log"
params:
extra="", # optional
java_opts="", # optional
wrapper:
"0.52.0/bio/gatk/splitncigarreads"
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. “-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¶
- Jan Forster
Code¶
__author__ = "Jan Forster"
__copyright__ = "Copyright 2019, Jan Forster"
__email__ = "jan.forster@uk-essen.de"
__license__ = "MIT"
import os
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' SplitNCigarReads {extra} "
" -R {snakemake.input.ref} -I {snakemake.input.bam} "
"-O {snakemake.output} {log}"
)