SNPSIFT VARTYPE¶
Add an INFO field denoting variant type.
Software dependencies¶
- snpsift =4.3.1t
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"
log:
"varType.log"
wrapper:
"0.59.1/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.
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
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
shell(
"SnpSift varType" # Tool and its subcommand
" {extra}" # Extra parameters
" {snakemake.input.vcf}" # Path to input vcf file
" > {snakemake.output.vcf}" # Path to output vcf file
" {log}" # Logging behaviour
)