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No need for optimizing that. I get that coming from embedded it might look fast and loose, but it won't be worthwhile to optimize everything as we go along. Later...

Ah, yeah, that is a quandary. Even with the warning the implication is that the first package is a binary because the later the source (thanks for clarifying though, it...

Thanks for the swift response. Our data can't leave the cluster and that cluster is even kept off the internet largely speaking (users connect through a VPN and then OVD...

I found another file with a similar structure to test on locally. Version 1.10.2 with htslib 1.10.2 is definitely wrong. 1.10.2-86-ge313e0f with htslib 1.10.2-86-g313a9fc appears to function correctly at least...

1.10.2-86-ge313e0f with htslib 1.10.2-86-g313a9fc functions correctly on the original file as well. Feel free to close this as soon as the documentation reflects that this does not actually work in...

@winni2k I may not be reading the code correctly, but I'm pretty sure it is doing empirical (i.e. genotyped) comparison only. That is, it uses GT (actual genotypes) only and...

@winni2k Sorry, yes they do. My internal convention of GT as genotyped slipped out because I don't usually use the imputed GT for comparison, though of course that is what...

@winni2k My apologies again. You are correct. I should stop mixing myself up. We are doing association from GT because those files are from whole-genome sequencing and are not imputed...

In general, the best way to convert from VCF to plink is to split multi-allelic sites, left align/normalize, give unique IDs, and then convert. This is described here: http://apol1.blogspot.com/2014/11/best-practice-for-converting-vcf-files.html The...

Yes, they are correcting for systemic bias independent of the trait in the sense that any association or lack thereof has no bearing on the MDS calculations. Once could substitute...