genpmda - Linux


genpmda generates a point mutation/deletion architecture file for annotating sequence variants. It is essential for the precise interpretation of genetic alterations in downstream analysis.


genpmda [options] <vcf-file> <output-file>


  • -h, –help: Display detailed help and usage information.
  • -v, –version: Print the current version of genpmda.
  • -o, –output-type: Specify the output format (default: "genpmda"). Other available formats: "json", "tsv", and "clinical".
  • -t, –type: Indicate the type of mutations to consider (default: "all"). Possible options: "substitutions", "indels", and "all".
  • –include-wildtype: Include wildtype alleles in the output (default: false).
  • -p, –padding: Set the padding size for flanks (default: 50).
  • -c, –context: Include the genomic context in the output (default: false).


Simple Usage:

genpmda my_variants.vcf variants.genpmda

Exclude Wildtype Alleles:

genpmda --include-wildtype=false my_variants.vcf variants.genpmda

Limit Mutations to Indels:

genpmda --type=indels my_variants.vcf indels.genpmda

Output in JSON Format:

genpmda --output-type=json my_variants.vcf variants.json

Common Issues

  • Error: VCF file not valid: Ensure the provided VCF file is formatted correctly and adheres to the VCF specification.
  • Error: Output file could not be created: Check write permissions in the output directory.


Annotating VCF Files:

grep -v ^"#" my_variants.vcf | genpmda -o json - | jq . > variants.json

Comparison of Mutation Architectures:

genpmda variants1.vcf arch1.genpmda
genpmda variants2.vcf arch2.genpmda
cmp arch1.genpmda arch2.genpmda

Related Commands