genpmda - Linux
Overview
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.
Syntax
genpmda [options] <vcf-file> <output-file>
Options/Flags
- -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).
Examples
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.
Integration
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