AstraZeneca-NGS/VarDict — pull request #1 by chapmanb (2014-07-27 10:58:20+00:00)
Title: Fixes for finding /usr/bin/env and FORMAT value preparation with BIAS

The recent changes to VarDict swapping `/usr/bin/env` to `/bin/env`
break execution on Ubuntu systems where `env` in only in `/usr/bin`. One
CentOS it is in both places, so `/usr/bin` seems like the more widely
supported path.

The recent bias change also causes issues by creating too many values.
GATK complains with:
```
The provided VCF file is malformed at approximately line number 52:
There are too many keys for the sample c-tumor, keys = GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM1/1:64:64:35,29:0,0:1:0:2:20.4:1:31.1:1:1:0:60:15:1:0:1.201/1:37:37:20,17:0,0:1:0:2:25.6:1:32.5:1:1:0:60:36:1:0:1.1,
```
Since swapping in colon separation creates 19 values and only 18 keys.
This swaps it back to using comma separation instead.