dajiangliu

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For gene level models, do they work with rare variants only (i.e., is it required to set --freqUpper 0.05)?

I agree that synonymous variants may not be considered lof. For some of our own work, we group variants that are nonsynonymous, stop_gain or splice [see e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709146/] The choice...

Segmentation fault when reading BGEN file

Did you try --meta score option? --single score is less actively maintained for now.

'setFile' format 0-based or 1-based ? refFlat: only exons ?

VCF is following 1-based, and we are following that. Thanks! All the best, Dajiang -- Associate Professor Co-Chair, Bioinformatics and Genomics Graduate Program Dept. Public Health Sciences Institute of Personalized...

License that applies to rvtests?

We follow GPL-3. We will find a time to add it. Thank you! All the best, Dajiang -- Associate Professor Dept. Public Health Sciences Institute of Personalized Medicine Penn State...

BGEN file does not work

We will surely take a look. Thanks for the comparisons. All the best, Dajiang -- Assistant Professor Dept. of Public Health Sciences Institute of Personalized Medicine Penn State College of...

BGEN file does not work

I think that the difference from PLINK can be due to the fact that PLINK uses hard genotype calls as input. If you give it a BGEN, it will first...