COMPRESS VCF

Compress and index vcf file with bgzip and tabix.

Software dependencies

  • htslib ==1.5

Example

This wrapper can be used in the following way:

rule compress_vcf:
    input:
        "{prefix}.vcf"
    output:
        "{prefix}.vcf.gz"
    wrapper:
        "0.19.2/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}")