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:
        "0.65.0/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

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}"
)