Hi everyone,

I am doing some variant calling in vcftools using the command below, and have noticed that the --max-missing function removes most of my data (it trims the vcf file from 32gb to 9kb). Dropping --max-miss to 0.8 raises the output file to 21.1 mb. What could be going on here? Any help is appreciated. Thanks.

vcftools --gzvcf xxx --remove-indels --maf 0.05 --max-missing 0.85 --minQ 30 --recode --stdout | gzip -c > xxx.filtered.vcf.gz