BCFTOOLS MERGE¶
Merge vcf/bcf files with bcftools. For more information see BCFtools documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule bcftools_merge:
input:
calls=["a.bcf", "b.bcf"]
output:
"all.bcf"
params:
"" # optional parameters for bcftools concat (except -o)
wrapper:
"0.85.0/bio/bcftools/merge"
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¶
bcftools=1.11
Authors¶
- Patrik Smeds
Code¶
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
shell(
"bcftools merge {snakemake.params} -o {snakemake.output[0]} "
"{snakemake.input.calls}"
)