BCFTOOLS VIEW¶
View vcf/bcf file in a different format.
Software dependencies¶
- bcftools ==1.5
Example¶
This wrapper can be used in the following way:
rule bcf_to_vcf:
input:
"{prefix}.bcf"
output:
"{prefix}.vcf"
params:
"" # optional parameters for bcftools view (except -o)
wrapper:
"0.31.0/bio/bcftools/view"
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¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
shell(
"bcftools view {snakemake.params} {snakemake.input[0]} "
"-o {snakemake.output[0]}")