COMPRESS VCF¶
Compress and index vcf file with bgzip and tabix.
Software dependencies¶
- htslib ==1.9
Example¶
This wrapper can be used in the following way:
rule compress_vcf:
input:
"{prefix}.vcf"
output:
"{prefix}.vcf.gz"
wrapper:
"0.38.0/bio/vcf/compress"
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 --stdout {snakemake.input} > {snakemake.output} && tabix -p vcf {snakemake.output}")