SNPSIFT GENES SETS
Annotate using GMT genes sets with SnpSift
Example
This wrapper can be used in the following way:
rule test_snpsift_gmt:
input:
call = "in.vcf",
gmt = "fake_set.gmt"
output:
call = "annotated/out.vcf"
# 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:
"v5.0.1/bio/snpsift/genesets"
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
bcftools=1.21
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
Calls that are to be annotated
A GMT-formatted annotation file
Output:
Annotated calls
Code
"""Snakemake wrapper for SnpSift geneSets"""
__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", "")
min_threads = 1
# Uncompression shall be done according to user-defined input
incall = snakemake.input["call"]
if snakemake.input["call"].endswith("bcf"):
min_threads += 1
incall = "< <(bcftools view {})".format(incall)
elif snakemake.input["call"].endswith("gz"):
min_threads += 1
incall = "< <(gunzip -c {})".format(incall)
# Compression shall be done according to user-defined output
outcall = snakemake.output["call"]
if snakemake.output["call"].endswith("gz"):
min_threads += 1
outcall = "| gzip -c > {}".format(outcall)
elif snakemake.output["call"].endswith("bcf"):
min_threads += 1
outcall = "| bcftools view > {}".format(outcall)
else:
outcall = "> {}".format(outcall)
# Each (un)compression step raises the threads requirements
if snakemake.threads < min_threads:
raise ValueError(
"At least {} threads required, {} provided".format(
min_threads, snakemake.threads
)
)
shell(
"SnpSift geneSets" # Tool and its subcommand
" {java_opts} {extra}" # Extra parameters
" {snakemake.input.gmt}" # Path to annotation vcf file
" {incall}" # Path to input vcf file
" {outcall}" # Path to output vcf file
" {log}" # Logging behaviour
)