### Get vcf2maf and maf2maf Manuals Source: https://github.com/mskcc/vcf2maf/blob/main/README.md View the detailed usage manuals for the vcf2maf and maf2maf scripts after installation. ```bash perl vcf2maf.pl --man perl maf2maf.pl --man ``` -------------------------------- ### Download and Install vcf2maf Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Download the latest release of vcf2maf, extract it, and navigate to the directory. This sets up the environment for using the scripts. ```bash export VCF2MAF_URL=$(curl -sL https://api.github.com/repos/mskcc/vcf2maf/releases | grep -m1 tarball_url | cut -d" -f4) curl -L -o mskcc-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf mskcc-vcf2maf.tar.gz; cd mskcc-vcf2maf-* ``` -------------------------------- ### vcf2maf with Custom VEP Paths Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Specify custom paths for VEP installation and cache data if they are not in the default locations. ```perl perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --vep-path /opt/vep --vep-data /srv/vep ``` -------------------------------- ### Clone and Build Docker Image Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Clone the vcf2maf repository and build a Docker image for local use. Ensure you have a recent version of Docker installed. ```bash git clone git@github.com:mskcc/vcf2maf.git cd vcf2maf docker build -t vcf2maf:main . docker builder prune -f ``` -------------------------------- ### Basic vcf2maf Conversion Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Convert a VCF file to a MAF file using vcf2maf. Ensure VEP is installed and configured. ```perl perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf ``` -------------------------------- ### Minimum Required Columns for maf2maf Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Illustrates the minimum set of columns required for input MAF or MAF-like files processed by maf2maf. ```text Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Tumor_Sample_Barcode 1 3599659 C T TCGA-A1-A0SF-01 1 6676836 A AGC TCGA-A1-A0SF-01 1 7886690 G A TCGA-A1-A0SI-01 ``` -------------------------------- ### Run vcf2maf script in Docker Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Execute the vcf2maf.pl script within a Docker container. Use the --help flag to see available options. ```bash docker run --rm vcf2maf:main perl vcf2maf.pl --help ``` -------------------------------- ### Download and Extract Test Data Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Manually fetch and extract the necessary VEP cache and FASTA files for testing. These are used to create a restricted test dataset. ```bash wget -P tests https://data.cyri.ac/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz gzip -d tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz wget -P tests https://data.cyri.ac/homo_sapiens_vep_112_GRCh38_chr21.tar.gz tar -zxf tests/homo_sapiens_vep_112_GRCh38_chr21.tar.gz -C tests ``` -------------------------------- ### Run maf2maf script in Docker Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Execute the maf2maf.pl script within a Docker container. Use the --help flag to see available options. ```bash docker run --rm vcf2maf:main perl maf2maf.pl --help ``` -------------------------------- ### Run Test Scripts Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Execute the provided Perl test scripts to verify the functionality of vcf2maf and its related tools. These scripts compare outputs against expected results. ```bash perl tests/vcf2maf.t perl tests/vcf2vcf.t perl tests/maf2vcf.t ``` -------------------------------- ### vcf2maf without VEP Annotation Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Generate a minimalist MAF-like file by skipping VEP annotation using the --inhibit-vep option. Use with caution, as MAF accuracy depends on upstream VEP processing. ```perl perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --inhibit-vep ``` -------------------------------- ### vcf2maf with Tumor and Normal IDs Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Specify tumor and normal sample IDs for filling MAF columns 16 and 17, and for parsing genotypes from matched columns in the VCF. ```perl perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --tumor-id WD1309 --normal-id NB1308 ``` -------------------------------- ### Basic maf2maf Reannotation Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Reannotate a MAF or MAF-like file using maf2maf. This process involves converting the MAF to VCF and then back to MAF. ```perl perl maf2maf.pl --input-maf tests/test.maf --output-maf tests/test.vep.maf ``` -------------------------------- ### vcf2maf with VarScan VCFs Source: https://github.com/mskcc/vcf2maf/blob/main/README.md Handle VCFs from variant callers like VarScan that use hardcoded sample IDs (e.g., TUMOR/NORMAL) in genotype columns. This ensures correct parsing while outputting proper sample IDs. ```perl perl vcf2maf.pl --input-vcf tests/test_varscan.vcf --output-maf tests/test_varscan.vep.maf --tumor-id WD1309 --normal-id NB1308 --vcf-tumor-id TUMOR --vcf-normal-id NORMAL ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.