tools/lh3misc/crap/denovo2vcf.lua

   1 #!/usr/bin/env luajit
   2
   3 require('klib')
   4
   5 -- convert Conrad et al. (2011) validation table to VCF
   6
   7 for l in io.lines() do
   8         local t = l:split('\t')
   9         if t[1] ~= 'id' then
  10                 local c = {t[15], t[16], t[11], t[12], t[13], t[14], t[39], t[40], 0, 0}
  11                 for i = 17, 38, 2 do
  12                         c[9], c[10] = c[9] + t[i], c[10] + t[i+1]
  13                 end
  14                 local tmp = t[5]:match('"(%S+)"')
  15                 if tmp ~= nil then t[5] = tmp end
  16                 if t[2] == '23' then t[2] = 'X' end
  17                 local o = {t[2], t[3], t[1], t[4], t[5]}
  18                 print(table.concat(o, '\t'), 30, '.',
  19                         'Type='..t[50]..';FLT='..t[51]..';Set='..t[6]..t[7]..t[8]..';CpG='..t[49],
  20                         'CUM:CSC',
  21                         c[1]..','..c[2]..':'..t[41]..','..t[42],
  22                         c[3]..','..c[4]..':'..t[43]..','..t[44],
  23                         c[5]..','..c[6]..':'..t[45]..','..t[46],
  24                         c[9]..','..c[10]..':'..t[47]..','..t[48],
  25                         c[7]..','..c[8]..':0,0')
  26         else
  27                 print('##fileformat=VCFv4.0')
  28                 print('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12878\tNA12891\tNA12892\tChildren\tNA12877')
  29         end
  30 end