vcftools QC process

Question

[chengyi31000]

I am going to have QC process of every CHR1 that I merge. I want to do HWE and call rate. Thant's waht I did with HEW process ./vcftools --vcf life_chr1.vcf --hwe 5e-8 --recode --out output_HWE

Is this right? the output_HWE is the final data??

How can I do with call rate process??(missing ratio)

Thank you very much!