GATK GENOTYPEGVCFS

Run gatk GenotypeGVCFs.

Example

This wrapper can be used in the following way:

rule genotype_gvcfs:
    input:
        gvcf="calls/all.g.vcf",  # combined gvcf over multiple samples
    # N.B. gvcf or genomicsdb must be specified
    # in the latter case, this is a GenomicsDB data store
        ref="genome.fasta"
    output:
        vcf="calls/all.vcf",
    log:
        "logs/gatk/genotypegvcfs.log"
    params:
        extra="",  # optional
        java_opts="", # optional
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024
    wrapper:
        "0.76.0/bio/gatk/genotypegvcfs"

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==4.2.0.0
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• GVCF files

Output:

• VCF file with genotypes

Notes

• The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
• The extra param allows for additional program arguments.
• For more information see, https://software.broadinstitute.org/gatk/documentation/article?id=11050

Authors

• Johannes Köster
• Jake VanCampen

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


import os

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)
interval_file = snakemake.input.get("interval_file", "")
if interval_file:
    interval_file = "-L {}".format(interval_file)
dbsnp = snakemake.input.get("known", "")
if dbsnp:
    dbsnp = "-D {}".format(dbsnp)

# Allow for either an input gvcf or GenomicsDB
gvcf = snakemake.input.get("gvcf", "")
genomicsdb = snakemake.input.get("genomicsdb", "")
if gvcf:
    if genomicsdb:
        raise Exception("Only input.gvcf or input.genomicsdb expected, got both.")
    input_string = gvcf
else:
    if genomicsdb:
        input_string = "gendb://{}".format(genomicsdb)
    else:
        raise Exception("Expected input.gvcf or input.genomicsdb.")
tmp_dir = snakemake.params.get("tmp_dir", "")
if tmp_dir:
    tmp_dir = "--tmp-dir={}".format(tmp_dir)

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

shell(
    "gatk --java-options '{java_opts}' GenotypeGVCFs {extra} "
    "-V {input_string} "
    "-R {snakemake.input.ref} "
    "{dbsnp} "
    "{interval_file} "
    "{tmp_dir} "
    "-O {snakemake.output.vcf} {log}"
)