Burden Test for whole exome sequencing data running into errors

Question

[shraimrawan]

Hi,

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)

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.