Variants analysed fewer than the input VCF's SNPs

[KarinaGuo]

Hi,

I wanted to ask a possibly naive question. Firstly, thank you in advance for your help I couldn't get much off of the web for this question.

As per the Issue's title suggests, I was wondering why when running the GWAS analysis using GEMMA, there are fewer variants analysed than that present in the input VCF. Specifically, the log states that there are only ~2 million variants analysed, whilst I know that the input VCF has ~33 million SNPs. There are no filtering options selected other than the vcf2gwas's option of --minaf 0.05. Attached is a relevant log. Hope this question makes sense, and thank you once again!

vcf2gwas_Mq_hwe_cat.beagle_GWAS_phenotype_height_COItransformedfoursqrt_20231023_054900.log.txt