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Validating repeat catalogs

Use trgt validate to validate a given TRGT repeat catalog relative to a reference genome before running trgt genotype. This is useful when you're developing your own repeat catalogs so issues get caught early. Every locus is analyzed, confirming that the coordinates are in bounds, and that the required annotations are present.

Inputs requirements

  • Reference genome (--genome): must point to the same FASTA file used during genotyping.
  • Repeat catalog (--repeats): accepts uncompressed or BGZF-compressed BED files. Each line must follow TRGT’s four-column format: chrom start end ID=<ID>;MOTIFS=<motif1,...>;STRUC=<structure>

What is validated?

Validation confirms that every contig name exists in the reference FASTA and that the repeat interval plus any requested flanks remain within sequence bounds. Whenever a locus fails validation, an error message is printed with the 1-based line number. Execution continues so you get a full list of issues in a single pass.

Example usage

trgt validate \
  --genome references/hg38.fa \
  --repeats catalogs/hg38_tr_catalog.bed.gz