calculate nucleotide forward and reverse reads from vcf

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?

vcf

• 1,850 views • link

written 10.2 years ago by bioguy24

1 answer

For anyone that may have a similar question, bam-read-count will give you numbers and a custom script should give you the output desired. Thank you :)

• 1 views • link

written 10.2 years ago by bioguy24