single_cohort_munge_variantlist

#!/bin/bash
fn=$1
mis=$2
maf=$3 
Rscript -e '
library(data.table)
d=fread("'$fn'", header=F)
setnames(d, c("chr", "ps", "ref", "alt", "ac", "an"))
MAFfromAF=function(x){
  out=x;out[x>0.5]=1-out[x>0.5]
  return(out)
}
d=d[ac>0,]
d[,af:=ac/an]
d[,maf := MAFfromAF(af)]
maxan=max(d[,an])*(1-'$mis');d=d[an>=maxan & maf<'$maf']
d[,id:="-"]
d=d[,c("chr", "ps", "id", "ref", "alt")]
fwrite(d, sub(".gz", ".formatted", "'$fn'"), sep="\t", col.names=F)'

bgzip ${fn/.gz/.formatted}
tabix -s 1 -b 2 -e 2 ${fn/.gz/.formatted.gz}