GATK SPLITNCIGARREADS

Run gatk SplitNCigarReads.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570487998491-SplitNCigarReads

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
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0/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. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).

• The extra param allows for additional program arguments.

Software dependencies

• gatk4=4.5.0.0

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• bam file

Output:

• split bam file

Authors

• Jan Forster

• Filipe G. Vieira

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2019, Jan Forster"
__email__ = "jan.forster@uk-essen.de"
__license__ = "MIT"

import os
import tempfile
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)

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' SplitNCigarReads"
        " --reference {snakemake.input.ref}"
        " --input {snakemake.input.bam}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output[0]}"
        " {log}"
    )