diempy: fast and reference-free genome polarisation

Le résumé fourni par la source

Abstract Most ancestry-assignment methods rely on putatively pure reference panels, which are often unrealistic and bias inference. The genome polarisation algorithm diem , introduced previously, avoids reference panels by jointly inferring the polarity of common allelic states and quantifying variant diagnosticity via an expectation–maximisation procedure. Here we present diempy , an efficient python implementation of diem coupled with tools that turn polarised calls into analysis-ready outputs. diempy offers lossless VCF-to- diem BED conversion; ploidy-aware handling of individuals and chromosomes; flexible masking of sites, regions and individuals; and interactive visualisation of polarised genomes, hybrid indices, clines and ternary plots. Post-processing functions include DI thresholding, kernel smoothing, and automatic detection and run-length encoding of contiguous ancestry tracts. BED-based I/O facilitates integration with population-genomic workflows (e.g. filtering by annotation or ploidy). These features make reference-free genome polarisation with diempy practical and reproducible for studies of population structure, admixture and species barriers.

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