In the GAPIT$GM results, some variant loci were identified where all sample genotypes were 0.

jiabowang / GAPIT

Genome Association Predict Integrate Tools

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In the GAPIT$GM results, some variant loci were identified where all sample genotypes were 0. #159

Open dozhun opened 3 weeks ago

dozhun commented 3 weeks ago

hi jiabo， During genotype processing with myGAPIT <- GAPIT(G=myHMP, output.numerical = TRUE, file.output = TRUE), I encountered an issue where some loci in the myGAPIT$GD results had all genotypes converted to 0. Additionally, the conversion between ref(to 0) and alt(to 2) alleles is not always consistent. Is there any specific setting or adjustment needed to address those conversion issues? I’ve attached my HMP file for reference. Thank you for your assistance!

demo.hmp.txt

jiabowang commented 3 weeks ago

Hi @dozhun Thanks for your report. I have fixed this error. Please try again with newest GAPIT function. source("https://raw.githubusercontent.com/jiabowang/GAPIT/refs/heads/master/gapit_functions.txt", encoding = "UTF-8")