I am trying to find a tool or script that can extract/calculate the base forward and reverse reads from a ion torrent vcf.gz.
Currently from NextGene we get output: (each base for a variant with the # of forward and reverse reads)
A(#F,#R) C(#F,#R) G(#F,#R) T(#F,#R) Ins(#F,#R) Del(#F,#R)
617;544 625;565 0;0 0;0 1;1 0;15
Maybe there are tags in the vcf, I'm not sure. The #'s in column J (format field) of the vcf are close:
0/1:4926:2359:2375:1186:1188:1171:1187:0.499789:551:620:622:564:567:620:622:566
but I am not sure. Thank you :).
edit: or should I use the bam to calculate the base reads and then match it to positions in the vcf?