chapmanb/bcbio-nextgen — pull request #465 by lpantano (2014-06-20 15:16:44+00:00)
Title: Convert FA to FREQ in FORMAT fields of MuTect VCFs

I did some easy substitutions to get FREQ instead of FA. Please, check if the output is what you expect (Just take the important lines):

```
##FORMAT=

chr22 222 . G T 0 PASS VT=SNP;SOMATIC GT:AD:BQ:DP:FREQ:SS 0/1:0,60:32:60:1.00:2 0:0,0:.:0:0.00:0
chr22 2211 . T C 0 PASS VT=SNP;SOMATIC GT:AD:BQ:DP:FREQ:SS 0/1:0,66:32:66:1.00:2 0:0,0:.:0:0.00:0
chr22 5090 . G T 0 REJECT . GT:AD:BQ:DP:FREQ 0/1:61,3:32:64:0.047 0:0,0:.:0:0.00
chr22 6025 . G T 0 PASS VT=SNP;SOMATIC GT:AD:BQ:DP:FREQ:SS 0/1:0,51:31:53:1.00:2 0:0,0:.:0:0.00:0
ch
```