genome-nexus / vcf2maf-lite

vcf2maf_lite

vcf2maf_lite is a lightweight Python adaptation of the vcf2maf Perl tool, designed to convert the VCF format to MAF format without adding variant annotations. For annotating a MAF file, Genome Nexus can be utilized.

Usage:

python3 vcf2maf_lite.py --help

  -i | --input-data             A list of .vcf files or input data directories, separated by commas [required]
  -o | --output-directory       output data directory [optional]
  -c | --center                 name of the center (standard MAF field = 'Center') [optional]
  -s | --sequence-source        Sequencing source (standard MAF field = 'Sequencing_Source'), e.g., WXS or WGS [optional]
  -t | --tumor-id               The ID of the tumor sample utilized in the genotype columns of the VCF file. [optional]
  -n | --normal-id              The ID of the normal sample utilized in the genotype columns of the VCF file. [optional]
  -a | --retain-info            Comma-delimited names of INFO fields to retain as extra columns in MAF [optional]
  -f | --retain-fmt             Comma-delimited names of FORMAT fields to retain as extra columns in MAF [optional]

Requirements

python 3

Running the tool example

python3 vcf2maf.py --input-data /data/vcf --output-directory /data/maf/ --center CTR --sequence-source WGS --tumor-id Tumor --normal-id Normal --retain-info Custom_filters,AC,AF,AC_nfe_seu,AC_afr,AF_afr --retain-fmt alt_count_raw,ref_count_raw,depth_raw

This command converts the VCF files in /vcf folder to MAF format.

• The --input-data option is used to specify either a single VCF file or a directory containing multiple VCF files (separated by commas). This option supports passing multiple input files or directories at once.
• The --output-directory option allows you to specify the directory where the MAF files will be saved. If no output path is provided, the default output directory vcf2maf_output will be used in the current working directory.
• The --tumor-id option allows you to specify the ID of the tumor sample used in the genotype columns of the VCF file. If the option is not used, the script will automatically identify the tumor ID from either the tumor_sample keyword in the meta data lines or the sample columns from VCF header.
• The --normal-id option allows you to specify the ID of the normal sample used in the genotype columns of the VCF file. If the option is not used, the script will automatically identify the normal ID from either the normal_sample keyword in the meta data lines or the sample columns from VCF header.
• The --retain-info option allows you to specify the INFO fields to be retained as additional columns in the MAF. If the option is not used, standard MAF columns are included by default.
• The --retain-fmt option allows you to specify the FORMAT fields to be retained as additional columns in the MAF. If the option is not used, standard MAF columns are included by default.

Convert with Docker

vcf2maf-lite is available in DockerHub at https://hub.docker.com/r/genomenexus/vcf2maf-lite

Usage:

docker pull genomenexus/vcf2maf-lite:main

docker run -v ${PWD}:/wd genomenexus/vcf2maf-lite:main python3 vcf2maf_lite.py --input-data /wd/test.vcf --output-directory /wd/maf/ --center CTR --sequence-source WGS --tumor-id Tumor --normal-id Normal --retain-info Custom_filters,AC,AF,AC_nfe_seu,AC_afr,AF_afr --retain-fmt alt_count_raw,ref_count_raw,depth_raw

• -v ${PWD}:/wd: This option maps the current working directory on local machine to the /wd directory inside the Docker container. This allows files in the local directory to be accessed from within the container.
• --input-data /wd/test.vcf: This option specifies the input file location at /wd/test.vcf.
• --output-directory /wd/maf/: This option specifies the output directory where the maf files will be saved. The files will be created at /wd/maf.

Resolving allele counts:

vcf2maf_lite supports the following VCF pipelines/methods for resolving the allele counts:

• VarScan
• SomaticSniper
• Strelka (SNPs and INDELs)
• CaVEMan
• Ion Torrent
• Delly
• cgpPINDEL
• MPileUp/BCFTools
• Other formats with the AD field
• ALT allele fractions

If none of the above apply, allele depths are set to empty strings.

Germline files

If germline is in the filename then vcf2maf_lite.py will assume that the file contains germline data. This will set the value in the output MAF Mutation_Status column to "GERMLINE". Please follow this naming convention if the mutation data file(s) are germline data.