VCF2VCF.PL

Reformat unconventional VCF

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

Example

This wrapper can be used in the following way:

rule test_vcf2vcf:
    input:
        vcf="small.vcf",
        fasta="small.fa",
        # Optional input files
        # chain="small.chain",
        # normal_bam="normal.bam",
        tumor_bam="tumor.bam",
    output:
        "corrected.vcf",
    threads: 1
    log:
        "test_vcf2vcf.log",
    params:
        extra=" --new-tumor-id ind2 ",
    wrapper:
        "v7.4.0/bio/vcf2maf/vcf2vcf"

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

This tool has no threading option.

Software dependencies

• vcf2maf=1.6.22

Input/Output

Input:

• vcf: Path to the VCF to reformat

• fasta: Path to a reference genome

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

• normal_bam: Optional path to normal bam file to overwrite DP:AD:ADF:ADR

• tumor_bam: Optional path to tumor bam file to overwrite DP:AD:ADF:ADR

Output:

• Path to corrected VCF file

Params

• extra: Optional parameters besides IO

Authors

Code

# coding: utf-8

"""This wrapper handles vcf2vcf.pl"""

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

from snakemake.shell import shell
from shlex import quote

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

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

normal_bam = snakemake.input.get("normal_bam")
if normal_bam:
    extra += f" --normal-bam={quote(normal_bam)}"

tumor_bam = snakemake.input.get("tumor_bam")
if tumor_bam:
    extra += f" --tumor-bam={quote(tumor_bam)}"

shell(
    "vcf2vcf.pl"
    " --input-vcf={snakemake.input.vcf:q}"
    " --ref-fasta={snakemake.input.fasta:q}"
    " {extra}"
    " --output-vcf={snakemake.output:q}"
    " {log}"
)