VCFTOOLS FILTER

Filter vcf files using vcftools

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:
        "v2.6.0/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.

Software dependencies

• vcftools=0.1.16

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}"
)