The problem of filtering snp parameters

[hhd1008611]

Hello sir,
Sorry to bother you;
I have a question about gemma's theory of analysis. How the gemma filter snps for analysis? because i noticed that too many snps wrere filterd during the analysis, can I change the filtering parameters?
Best regards.

[297B1]

Hello! Is your problem solved? There are some instructions in the 'SNP filters' section of the GEMMA User Manual, but some of the SNPs in my file that don't meet the filter criteria are also filtered out. I would like to ask what could be the reason?
Best regards.

[hlnicholls]

Hi, I have also ran into this problem with running GEMMA, has there been any solution beyond the manual's SNP filter parameters?

I QC my genotype file for missingness, pruning, HWE etc. before running GEMMA, then turn off all SNP filters that account for these in GEMMA, and add a SNP list of all my SNPs, but on analysis GEMMA still cuts down ~70-80% of SNPs in the file.

I have tried going to the google group for discussions around this topic (https://groups.google.com/access-error?continue=https://groups.google.com/g/gemma-discussion) but it just loads a page saying "content unavailable"