VEP (Variant Effect Predictor) predicts the functional effects of genomic variants. The annotated VCF will be converted into MAF based on vcf2maf.
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  1. {
  2. "vep_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/vep:v104.0",
  3. "fasta": "GRCh38.d1.vd1.fa",
  4. "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
  5. "cache": "oss://pgx-reference-data/ensembl_vep/",
  6. "vep_path": "/opt/vep/ensembl-vep",
  7. "species": "homo_sapiens_merged",
  8. "ncbi_build": "GRCh38",
  9. "vcf2maf_path": "/opt/mskcc-vcf2maf",
  10. "disk_size": "200",
  11. "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
  12. }