Dear Martin, and all, 

would like to ask for an advice about the use of the function subsetByFilter(vcf, filter). 

I have the following piece of R code that is working (below) -- thanks Martin for suggestions !

vcf <- readVcf("AML_out.vcf.bgzip",genome="hg38")

AFADfilter = function(x) {
            af <- geno(x)$AF[,"TUMOR"] > 0.05
            ad <- sum(as(geno(x)$AD[,"TUMOR"], "List")) >= 5
            af & ad
                         }

z <- vcf[AFADfilter(vcf)]
writeVcf(z,"output.vcf")

However, if I want to use the function subsetByFilter(), there is an error message :

subsetByFilter(vcf, filter=AFADfilter)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘subsetByFilter’ for signature ‘"CollapsedVCF", "function"’

The filter argument is supposed to be a FilterRules object, so

subsetByFilter(vcf, filter=FilterRules(list(AFADfilter=AFADfilter)))