VEMBRANE TABLE
Vembrane table allows to generate table-like textfiles from vcfs based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN. When filtering based on ANN, annotation entries are filtered first. https://github.com/vembrane/vembrane
Example
This wrapper can be used in the following way:
rule vembrane_table:
input:
vcf="in.vcf",
output:
vcf="table/out.tsv"
params:
expression="CHROM, POS, ALT, REF",
extra=""
log:
"logs/vembrane.log"
wrapper:
"v5.0.1/bio/vembrane/table"
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
vembrane=1.0.7
Input/Output
Input:
A VCF-formatted file
Output:
A table-like textfile
Code
"""Snakemake wrapper for vembrane"""
__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
shell(
"vembrane table" # Tool and its subcommand
" {extra}" # Extra parameters
" {snakemake.params.expression:q}"
" {snakemake.input}" # Path to input file
" > {snakemake.output}" # Path to output file
" {log}" # Logging behaviour
)