BCFTOOLS INDEX¶
Index vcf/bcf file. For more information see BCFtools documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule bcftools_index:
input:
"a.bcf"
output:
"a.bcf.csi"
params:
extra="" # optional parameters for bcftools index
wrapper:
"v1.3.1/bio/bcftools/index"
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¶
- Jan Forster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
## Extract arguments
extra = snakemake.params.get("extra", "")
shell("bcftools index {extra} {snakemake.input[0]} {log}")