Hello- I'm using GEMMA for the first time and having difficulty generating a kinship matrix. From the output, it seems like the files are being read, but for some reason all 2 million SNPs are not passing some internal threshold. I looked at the minor allele frequencies for these SNPs and the majority are well over the 1% cutoff, so I don't think it's that. I've also tried altering the
-miss and -r2 terms, and these also don't seem to help retain any SNPs.
Any help would be appreciated!
Thank you,
Jenn
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
Hello- I'm using GEMMA for the first time and having difficulty generating a kinship matrix. From the output, it seems like the files are being read, but for some reason all 2 million SNPs are not passing some internal threshold. I looked at the minor allele frequencies for these SNPs and the majority are well over the 1% cutoff, so I don't think it's that. I've also tried altering the -miss and -r2 terms, and these also don't seem to help retain any SNPs.
Any help would be appreciated! Thank you, Jenn
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ...
number of total individuals = 45
number of analyzed individuals = 45
number of covariates = 1
number of phenotypes = 1
number of total SNPs/var = 2088745
number of analyzed SNPs = 0
Calculating Relatedness Matrix ... ================================================== 100%