How to set the missing rate during filtering---gatk VariantFiltration

[dongyiyi]

Hi all,

I am using gatk VariantFiltration to filter my GBS data. I need to set a threshold for the missing rate, such as 0.7. I know I can use vcftools -max-missing 0.7, and then I can further use other parameters to filter: --maf; --max-maf; --min-alleles; --max-alleles. I try to perform the same code via gatk code, and I went through the official doc on the gatk website, which does not list all information, or it does, and I have a hard time understanding the arguments. I found some potential parameters, but I don't really know which one is the correct parameter. --max-filtered-genotypes: Maximum number of samples filtered at the genotype level; --max-fraction-filtered-genotypes: Maximum fraction of samples filtered at the genotype level; --max-nocall-fraction: Maximum fraction of samples with no-call genotypes;

Thanks!