GATK LEFTALIGNANDTRIMVARIANTS

Run gatk LeftAlignAndTrimVariants

URL: https://gatk.broadinstitute.org/hc/en-us/articles/360037225872-LeftAlignAndTrimVariants

Example

This wrapper can be used in the following way:

rule gatk_leftalignandtrimvariants:
    input:
        vcf="calls/test_split_with_AS_filters.vcf",
        ref="Homo_sapiens_assembly38.chrM.fasta",
        fai="Homo_sapiens_assembly38.chrM.fasta.fai",
        dict="Homo_sapiens_assembly38.chrM.dict",
#       intervals="intervals.bed", # optional
    output:
        vcf="calls/split_multiallelics.vcf",
    log:
        "logs/gatk/leftalignandtrimvariants.log",
    params:
        extra="--split-multi-allelics", # optional
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.9.0-1-gc294552/bio/gatk/leftalignandtrimvariants"

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:

• A variant call set to left-align and trim

Output:

• A left-aligned VCF

Authors

• Dmitry Bespiatykh

Code

"""Snakemake wrapper for GATK LeftAlignAndTrimVariants"""

__author__ = "Dmitry Bespiatykh"
__copyright__ = "Copyright 2023, Dmitry Bespiatykh"
__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)


intervals = snakemake.input.get("intervals", "")
if not intervals:
    intervals = snakemake.params.get("intervals", "")
if intervals:
    intervals = "--intervals {}".format(intervals)


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' LeftAlignAndTrimVariants"
        " --variant {snakemake.input.vcf}"
        " --reference {snakemake.input.ref}"
        " {intervals}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.vcf}"
        " {log}"
    )