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=<ID=FREQ,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">

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
```
`readlines()` reads the whole file into memory, which is not what we want in case of large VCFs. You could use 

````python
for line in handle:
````
Also as a suggestion you may want to short-circuit the loop by avoiding the replacements / searches if the line doesn't start by #:

````python
if line.startswith("#"):
    # Put rest of code here
writer.write(line)
````