VariantsToTable allows you to use "-SMA" to split multi-allelic variants into multiple rows. I am trying to work it on ExAC vcf (0.3.1) files. It works for AC, AN field in the INFO tag, but not for AC_Het, AC_Hom and any population specific denoted by Het and Hom such as Het_FIN and Hom_FIN. I understand flags like Het_*** and Hom_*** is not a common flags for most VCF files. I wonder if there is a way that VariantsToTable can take care all field in the INFO tag with multiple entries.
CHROM POS ID REF ALT QUAL FILTER NCC AN AC AF AN_Adj AC_Adj AC_Het AC_Hom
1 2337157 rs1143017 C G 347.4 PASS 1444 120044 1 0.000008 37642 1 1 0
1 2337161 . C T 80.05 AC_Adj0_Filter 1393 120078 1 0.000008 37822 0 0 0
1 2337162 . TC T 40066.58 PASS 1384 120090 15 0.000125 37962 11 11 0
1 2337164 . CCGTA C 8706.97 PASS 1352 120116 22 0.000183 37976 13 13 0
1 2337165 . C T 1357.97 PASS 1355 120102 4 0.000033 38014 2 2 0
1 2337166 . G A 576.12 PASS 1316 120154 5 0.000042 38198 2 2,1,0 0
1 2337166 . G T 576.12 PASS 1316 120154 1 0.000008 38198 1 2,1,0 0