- Find Parentage, Validate Pedigree and PolyBreedTools now accept genotypes as text files (.txt/.csv), VCF files (.vcf/.vcf.gz), or ‘PLINK’ .ped files, in addition to the previous tab-separated format. VCF calls are converted to allele-B dosages using the selected Ploidy; .ped files are diploid only.
- PolyBreedTools: a .map upload appears for each .ped genotype file so markers are matched by name. If either genotype file is a .ped, both must be; the validation .ped is coded with the reference panel’s counted allele per marker.
- PolyBreedTools: new Assignment threshold (%) input. Samples whose highest line proportion is below the threshold are labeled “Undetermined”. Changes apply without re-running the estimation. The default is 50; use 0 to always assign the highest line.
- SNMF: the plot, Q matrix and downloads use the best (lowest cross-entropy) run for the selected K by default. The manual run selector moved to an Advanced Options dialog for diagnostics; changing K or re-running resets to the best run. The Help panel now explains run selection.
- Updated the in-app Instructions and Help panels for the new input formats.
- Column names
id,male_parent,female_parentandsexin uploaded files are no longer case sensitive (e.g.ID,Male_Parentare accepted). - VCF uploads (all modules, including SNMF) now stop with a clear message when the selected Ploidy differs from the most common ploidy in the file, and suggest the ploidy to use (e.g. “The VCF looks tetraploid (ploidy 4) … Set Ploidy to 4 and run again.”).
- Fixed “Save Image” downloads: the file type is set explicitly, svg export works without the ‘svglite’ package, and saving errors are shown in the app.
- Requires ‘BIGpopA’ (>= 2.1.0).
Release on GitHub · About Familia
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