GATK COLLECTREADCOUNTS

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/gatk/collectreadcounts?label=version%20update%20pull%20requests

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/360037592671-CollectReadCounts

Example

This wrapper can be used in the following way:

rule collectreadcounts:
    input:
        bam=["mapped/a.bam"],
        intervals=["a.interval_list"],
    output:
        counts="a.counts.hdf5",
    log:
        "logs/gatk/collectreadcounts.log",
    params:
        extra="",  # optional
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0-1-g149ef14/bio/gatk/collectreadcounts"

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=4.5.0.0

  • snakemake-wrapper-utils=0.6.2

Input/Output

Input:

  • bam: BAM/SAM/CRAM file containing reads

  • intervals: one or more genomic intervals over which to operate

Output:

  • counts: output file for read counts, tsv or hdf5

Params

  • mergingRule: interval merging rule for abutting intervals (default, OVERLAPPING_ONLY)

  • java_opts: 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).

  • extra: additional program arguments.

Authors

  • Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2023, Patrik Smed"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"


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)

mergingRule = snakemake.params.get("mergingRule", "OVERLAPPING_ONLY")

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

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' CollectReadCounts"
        " -I {snakemake.input.bam}"
        " -L {snakemake.input.intervals}"
        " --interval-merging-rule {mergingRule}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.counts}"
        " {log}"
    )