Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Support mixed ploidy in display_genotypes

See original GitHub issue

Currently a lower ploidy sample appears to have missing alleles i.e. -2 is treated as -1. The the calls [[0, 0, 1, 1], [0, 1, -2, -2], [0, 0, 1, -1]] would ideally be displayed as 0/0/1/1 0/1 0/0/1/. in a mixed-ploidy dataset.

Issue Analytics

State:
Created 2 years ago
Comments:6

Top GitHub Comments

1reaction

timothymillarcommented, Jun 3, 2021

Defaulting to the most human readable option makes sense. I’m interested to see what that option would look like!

1reaction

jeromekellehercommented, Jun 2, 2021

Sorry I was being unclear @timothymillar - I just meant that people might think there’s phase information encoded in there as well if we’re following the VCF way of doing things.

Maybe we could use some unicode box drawing characters to help display things more effectively? This is a “human only” encoding, so maybe we could do something a bit nicer if we’re not restricted to ASCII?

Top Results From Across the Web

Mixed-Ploidy Species: Progress and Opportunities ... - PubMed

Mixed -ploidy species harbor a unique form of genomic and phenotypic variation that influences ecological interactions, facilitates genetic divergence, ...

Tracing evolutionary history and admixture in mixed‐ploidy ...

(2021) develops the first software specifically designed to infer population structure and ancestry in large genome-wide mixed-ploidy data ...

The mechanism of constructing mixed-ploidy populations in ...

Background & Aims: Polyploidization, the duplication of entire genomes, is a key driver in the processes of speciation and evolution, and almost all...

Single Independent Autopolyploidization Events From Distinct ...

Supporting the PCoA, the two mixed-ploidy populations (Hojs456/2Q and Hojs487/2Y) falling out of the diploid clustering (Figure 4, ...

Model-based genotype and ancestry estimation for potential ...

models for polyploid and mixed-ploidy individuals and populations has ... study of systems for which K = 2 was well supported, the ancestry ......