Re-add the muTect file (messy history)
Add support for MuTect in the BroadRunner, and change from_config to
also use the name of the program (defaults to "gatk" for backwards
compatibility)
Adapt the MuTect support to the newest changes in bcbio-nextgen
Add MutTect to the available callers
Fix parameter order
Use the sample name from the items
Small adjustment to the name
Explicitly ask for the MuTect jar
Merge remote-tracking branch 'upstream/master' into mutect
First attempt at trying to ignore one specific MuTect error until the
issue in MuTect itself is resolved
Merge branch 'mutect' of github.com:cswegger/bcbio-nextgen into mutect
Parse the Java stack trace from the error in MuTect and adjust the
check accordingly
Try to be even more specific: catch *only* the error caused by the
MuTect issue / bug, and keep everything else as-is
- Catch more similar exceptions just in case
- Use the right file when writing out an empty file
- Add parameter for fraction contamination (impure tumors)
Remove usage of -nt, it's not really supported by MuTect
Merge pull request #40 from lbeltrame/mutect

Initial support for the MuTect tumor/normal calling algorithm