GATK COLLECTALLELICCOUNTS

Collects reference and alternate allele counts at specified sites.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/13832754187035-CollectAllelicCounts

Example

This wrapper can be used in the following way:

rule collectalleliccounts:
    input:
        bam=["mapped/a.bam"],
        intervals=["a.interval_list"],
        ref="ref/genome.fasta"
    output:
        counts="a.counts.tsv",
    log:
        "logs/gatk/collectalleliccounts.log",
    params:
        extra="",  # optional
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.9.0-14-g476823b/bio/gatk/collectalleliccounts"

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

• ref: reference FASTA file

Output:

• counts: tab-separated values (TSV) file with allelic counts and a SAM-style header

Params

• 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)

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

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' CollectAllelicCounts"
        " -I {snakemake.input.bam}"
        " -L {snakemake.input.intervals}"
        " -R {snakemake.input.ref}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.counts}"
        " {log}"
    )