VARLOCIRAPTOR CONTROL FDR

Control false discovery rate of Varlociraptor calls

URL: https://varlociraptor.github.io/docs/filtering/

Example

This wrapper can be used in the following way:

rule varlociraptor_control_fdr:
    input:
        "results/variant-calls/{sample_group}.bcf",
    output:
        "results/variant-calls/{sample_group}.fdr-controlled.bcf",
    log:
        "logs/varlociraptor/control-fdr/{sample_group}.log",
    params:
        fdr=0.05,
        mode="local-smart",
        events=["present"],  # list of event names that occur in BCF (case-insensitive)
    wrapper:
        "v5.5.2-17-g33d5b76/bio/varlociraptor/control-fdr"

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

• varlociraptor=8.6.0

Input/Output

Input:

• BCF/VCF file with Varlociraptor calls

Output:

• filtered BCF/VCF file with Varlociraptor calls such that given FDR is not exceeded

Authors

• Johannes Köster

Code

import subprocess as sp

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

sp.run(
    "varlociraptor filter-calls control-fdr "
    f"{snakemake.input[0]} "
    f"--mode {snakemake.params.mode} "
    f"--fdr {snakemake.params.fdr} "
    f"--events {' '.join(snakemake.params.events)} "
    f"> {snakemake.output[0]} {log}",
    check=True,
    shell=True,
)