what are valid SNPs?

Hi 

Could you point me to why only half of my SNPs are valid ?  I cannot find any mention of default filtering values.
There are only autosomes in the dataset.

How do I generate a list if valid SNPs

 

/gcta_v1.94.0Beta_linux_kernel_3_x86_64_static --bfile 9folders_filtered_nodup --make-grm --out 9folders_filtered_nodup


log 

126847 SNPs have been processed.
Used 67540 valid SNPs.
The GRM computation is completed.
Saving GRM...

Thanks

Guy