UNCOMPRESS VCF¶
Uncompress vcf file with bgzip.
Software dependencies¶
- htslib ==1.9
Example¶
This wrapper can be used in the following way:
rule uncompress_vcf:
input:
"{prefix}.vcf.gz"
output:
"{prefix}.vcf"
wrapper:
"0.37.0/bio/vcf/uncompress"
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("bgzip --decompress --stdout {snakemake.input} > {snakemake.output}")