VARSCAN SOMATIC
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:
"v3.4.1/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
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
)