SNPSIFT VARTYPE

Add an INFO field denoting variant type with SnpSift

Example

This wrapper can be used in the following way:

rule test_snpsift_vartype:
    input:
        vcf="in.vcf"
    output:
        vcf="annotated/out.vcf"
    message:
        "Testing SnpSift varType"
    # 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
    log:
        "varType.log"
    wrapper:
        "v3.0.0/bio/snpsift/varType"

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

• snpsift=5.2

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• A VCF-formatted file

Output:

• A VCF-formatted file

Authors

• Thibault Dayris

Code

"""Snakemake wrapper for SnpSift varType"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2020, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")

shell(
    "SnpSift varType"  # Tool and its subcommand
    " {java_opts} {extra}"  # Extra parameters
    " {snakemake.input.vcf}"  # Path to input vcf file
    " > {snakemake.output.vcf}"  # Path to output vcf file
    " {log}"  # Logging behaviour
)