Marnin Wolfe

Just wanted to link this to the issue on allele dosages in VCFs: https://github.com/solgenomics/sgn/issues/3906

Perhaps. "Expected Max NOHAV" would probably be the same for all plots in a given trial, but you never know. On Mon, Sep 12, 2022 at 9:42 AM Lukas Mueller...

Dangerous, I agree. I do this only with care and knowledge. However, here's an example of why: There is a genotyping protocol "West Africa 2020" that has the NRCRI training...

> Yeah I am struggling with the same issue. My solution is to impute everything to the same genotyping protocol. It's a bit of a pain, but you would need...

> > Dangerous, I agree. I do this only with care and knowledge. > > Would you elaborate on the care and knowledge you apply? Well my whole pipeline for...

Something akin to a dosage matrix but representing haplotypes. Here is what I've done, extracting haplotypes from a VCF: https://wolfemd.github.io/IITA_2021GS/04-PreprocessDataFiles.html#Haplotype_matrix_from_phased_VCF Uses `bcftools convert --hapsample` You can also see the input...