It was called to my attention that base calls denoted "." in VCF are mapped to REF instead of missing. This has been repaired in release and devel. The solution is to map the genotype to missing (raw 0) if any base is denoted ".". Owing to issues with dependencies and the build system, it may take time for the devel version repair to emerge. For those working with source, the patch is --- vcfutils.R (revision 56128) +++ vcfutils.R (working copy) @@ -45,9 +45,10 @@ meta = vec[1:nmetacol] calls = vec[-c(1:nmetacol)] nalt = strsplit(calls, "") - nums = lapply(nalt, "[", c(1,3)) - nalt = sapply(nums, function(x) 2-sum(x=="0")) - if anyis.na(nalt))) nalt[whichis.na(nalt))]=-1 + nums = lapply(nalt, "[", c(1,3)) # extract the call components + hasmiss = which(sapply(nums, function(x) any(x == "."))) + nalt = sapply(nums, function(x) 2-sum(x=="0")) # this is correct only for diallelic locus; note in doc + if (length(hasmiss)>0) nalt[hasmiss] = -1 nalt = nalt+1 chr = meta[1] id = meta[3] At this time I personally am not making extensive use of VCF so observations of shortcomings of this functionality are welcome. At present the function makes no use of call uncertainty information, and it is hoped this will be remedied before too long.