VARSCAN SOMATIC

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

Varscan Somatic calls variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair.

Example

This wrapper can be used in the following way:

rule varscan_somatic:
    input:
        # A pair of pileup files can be used *instead* of the mpileup
        # normal_pileup = ""
        # tumor_pileup = ""
        mpileup = "mpileup/{sample}.mpileup.gz"
    output:
        snp = "vcf/{sample}.snp.vcf",
        indel = "vcf/{sample}.indel.vcf"
    message:
        "Calling somatic variants {wildcards.sample}"
    threads:
        1
    # 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
    params:
        extra = ""
    wrapper:
        "v3.9.0/bio/varscan/somatic"

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

  • varscan=2.4.6

  • snakemake-wrapper-utils=0.6.2

Input/Output

Input:

  • A pair of pileup files (Normal/Tumor)

Output:

  • A VCF file

Authors

  • Thibault Dayris

Code

"""Snakemake wrapper for varscan somatic"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2019, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"


import os.path as op

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

# Defining logging and gathering extra parameters
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

# Building output dirs
makedirs(op.dirname(snakemake.output.snp))
makedirs(op.dirname(snakemake.output.indel))

# Output prefix
prefix = op.splitext(snakemake.output.snp)[0]

# Searching for input files
pileup_pair = ["normal_pileup", "tumor_pileup"]

in_pileup = ""
mpileup = ""
if "mpileup" in snakemake.input.keys():
    # Case there is a mpileup with both normal and tumor
    in_pileup = snakemake.input.mpileup
    mpileup = "--mpileup 1"
elif all(pileup in snakemake.input.keys() for pileup in pileup_pair):
    # Case there are two separate pileup files
    in_pileup = " {snakemake.input.normal_pileup}" " {snakemakeinput.tumor_pileup} "
else:
    raise KeyError("Could not find either a mpileup, or a pair of pileup files")

shell(
    "varscan somatic"  # Tool and its subcommand
    " {in_pileup}"  # Path to input file(s)
    " {prefix}"  # Path to output
    " {java_opts} {extra}"  # Extra parameters
    " {mpileup}"
    " --output-snp {snakemake.output.snp}"  # Path to snp output file
    " --output-indel {snakemake.output.indel}"  # Path to indel output file
)