VCFTOOLS FILTER

Filter vcf files using vcftools

Software dependencies

  • vcftools ==0.1.15

Example

This wrapper can be used in the following way:

rule filter_vcf:
    input:
        "{sample}.vcf"
    output:
        "{sample}.filtered.vcf"
    params:
        extra="--chr 1 --recode-INFO-all"
    wrapper:
        "0.27.0/bio/vcftools/filter"

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

  • Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell

input_flag = "--vcf"
if snakemake.input[0].endswith(".gz"):
    input_flag = "--gzvcf"

output = " > " + snakemake.output[0]
if output.endswith(".gz"):
    output = " | gzip" + output

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

extra = snakemake.params.get("extra", "")

shell("vcftools "
      "{input_flag} "
      "{snakemake.input} "
      "{extra} "
      "--recode "
      "--stdout "
      "{output} "
       "{log}")