PRE.PY

Preprocessing/normalisation of vcf/bcf files. Part of the hap.py suite by Illumina (see https://github.com/Illumina/hap.py/blob/master/doc/normalisation.md).

Example

This wrapper can be used in the following way:

rule preprocess_variants:
    input:
        ##vcf/bcf
        variants="variants.vcf",
    output:
        "normalized/variants.vcf.gz",
    log:
        "log/pre.log",
    params:
        ## path to reference genome
        genome="genome.fasta",
        ## parameters such as -L to left-align variants
        extra="-L",
    threads: 2
    wrapper:
        "v4.6.0/bio/hap.py/pre.py"

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

• hap.py=0.3.15

Authors

• Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2019, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"

from os import path

from snakemake.shell import shell

## Extract arguments
extra = snakemake.params.get("extra", "")

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

shell(
    "(pre.py"
    " --threads {snakemake.threads}"
    " -r {snakemake.params.genome}"
    " {extra}"
    " {snakemake.input.variants}"
    " {snakemake.output})"
    " {log}"
)