zhanxw

Can you please remind me the number of sites specified by `--siteFile` option? Just want to confirm that with you, as I guess that very large amount of sites slows...

@jiehuang001 I have optimized `--siteFile` option to improve speed. However, you may consider using `--rangeFile` instead. Since you have a small amount of variants (93 variants) to analyze, I would...

I did not explicitly support PLINK binary files as VCF files can represent more types of genetic data (e.g., genotypes and dosages). Actually, you can convert PLINK binary file to...

Hi Carolina, Usually you can safely ignore this warning. Let me check once more to make sure of that. Thanks. Xiaowei

Hi Zishan, Can you please check how many columns in the chrx kinship matrix file? Thanks.

The extra column of IID may be the reason of 'Extra column Kinship matrix'.

@dajiangliu We have implemented this option, but need some more tests.

I have examined codes and have not found obvious problems. Are the negative AF close to zero? Are those variant sites singletons?

@jiehuang001 is it possible you can post the log file here? I have tried many ways to debug this issue, but am still stuck.

The default frequency calculation method is changed in this version (https://github.com/zhanxw/rvtests/releases/tag/v2.0.6). The AF is just half of the mean genotypes/dosages, and it should be positive all the time now.