BCFTOOLS CONCAT¶
Concatenate vcf/bcf files with bcftools.
Software dependencies¶
- bcftools ==1.5
Example¶
This wrapper can be used in the following way:
rule bcftools_concat:
input:
expand("called/{region}.bcf", region=chromosomes)
output:
"called/all.bcf"
params:
"" # optional parameters for bcftools concat (except -o)
wrapper:
"0.19.1/bio/bcftools/concat"
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 concat {snakemake.params} -o {snakemake.output[0]} "
"{snakemake.input}")