I am trying to run a burden test on vcf files using PLINK SEQ. When running the program, I run into the error when trying to get the gene based associations. My code is posted below, and the error is posted below. Any help would be appreciated.
I ran gatk on my vcf file to filter out low quality variants. Then fed that file into plink seq
pseq "vcf.file" assoc --phenotype phe1 --mask loc.group=refseq > burdentest.txt Error: plinkseq warning: convergence problem in tqli() (repeated 3103 times)