VCF2MAF.PL

Convert a VCF into a MAF

URL: https://github.com/mskcc/vcf2maf/tree/main?tab=readme-ov-file#vcfmaf

Example

This wrapper can be used in the following way:

rule test_vcf2maf:
    input:
        # Optional external VEP install
        # vep="path/to/vep/bin",
        # vep_cache="path/to/vep_cache",
        # vep_config="vep.config",
        vcf="small.vcf",
        # Optional input files
        # chain="small.chain",
        fasta="small.fa",
    output:
        "small.maf",
    threads: 1
    log:
        "test_vcf2maf.log",
    params:
        extra=" --tumor-id ind1 --normal-id NORMAL ",
    wrapper:
        "v7.5.0/bio/vcf2maf/vcf2maf"

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.

Notes

In order to use VEP in this wrapper, user must provide an external VEP binary, cache and/or configuration. If none of the VEP-related input parameters are filled, this wrapper automatically turns Ensembl VEP options off.

This wrapper uses only one thread if Ensembl VEP is turned off.

Software dependencies

• vcf2maf=1.6.22

Input/Output

Input:

• vcf: Path to the VCF to reformat

• fasta: Optional path to a reference genome

• chain: Optional chain file to remap variants to a different assemnly

• vep: Optional path to a Ensembl VEP install directory

• vep_cache: Optional path to Ensembl VEP cache

• vep_config: Optional path to Ensembl VEP configuration file

Output:

• Path to MAF file

Params

• extra: Optional parameters besides IO and temporary directory

Authors

Code

# coding: utf-8

"""This wrapper handles vcf2maf.pl"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2020, Thibault Dayris"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from tempfile import TemporaryDirectory
from snakemake.shell import shell
from warnings import warn
from shlex import quote

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

# Optional input files
fasta = snakemake.input.get("fasta")
if fasta:
    extra += f" --ref-fasta={quote(fasta)}"

chain = snakemake.input.get("chain")
if chain:
    extra += f" --remap-chain={quote(chain)}"

# Acquiring external VEP installation (if any)
vep = ""
vep_path = snakemake.input.get("vep", "")
if vep_path:
    vep = f"--vep-path={quote(vep_path)}"

vep_config = snakemake.input.get("vep_config")
if vep_config:
    vep += f" --vep-config={quote(vep_config)}"

vep_cache = snakemake.input.get("vep_cache")
if vep_cache:
    vep += f" --vep-data={quote(vep_cache)}"

# Automatically turning VEP off if user
# does not provide at least one VEP information
if all([vep_path, vep_cache, vep_config]):
    # vcf2maf.pl can run VEP using more than one thread
    # This would be the only multithreaded section of the code
    vep += f" --vep-forks={snakemake.threads}"
else:
    vep = "--inhibit-vep"
    if snakemake.threads > 1:
        warn("Too many threads requested: only 1 used.")

# Autmatically set temporary directory
with TemporaryDirectory() as tempdir:
    shell(
        "vcf2maf.pl"
        " --input-vcf={snakemake.input.vcf:q}"
        " {vep}"
        " {extra}"
        " --tmp-dir={tempdir:q}"
        " --output-maf={snakemake.output:q}"
        " {log}"
    )