Add SOMATIC flag for FreeBayes records

Initial step to address issue #317, but it is not hooked yet to the pipeline
Merge branch 'master' into vcf-somatic-fix
Hook the somatic fixing to Freebayes's paired pipeline and make the move
be in place
Document rebooted sequencer integration and remove replaced deprecated functionality
Remove unused sequencer integration scripts after new approach in place. Clean up utility scripts unrelated to main bcbio-nextgen functionality
Skip detecting Broad programs -- GATK, Picard, MuTecT if not present during initial provenance/version check. #375
Skip detecting Broad programs -- GATK, Picard, MuTecT if not present during initial provenance/version check. #375
Sequencer support: ensure we right message database to avoid double runs when on cronjob. Fix PATH in example cronjob
Update human resources to include 1000 genomes high confidence SNPs used for VQSR
GATK VQSR update and reorganization. Clean up code and move into own namespace. Update to latest best practice recommendations
Refactor GATK specific calling code into separate namespace. Cleans up GATK based called for future 3.x integration. #348
Code cleanup: remove old sequencer integration code. Remove bigwig generation; fixes #195
Avoid running program checks when we're not running a downstream analysis. #375
Initial framework for supporting Clusterk/AWS parallelization
Clarify supported infrastructures for sequencer integration: HiSeqs dumping to Linux machines. Fixes #381
Pass along core and memory requirements for clusterk parallel
Modified SID settings to allow up to 10k coverage and lowered AF threshold to 0.5%
Merge pull request #384 from mjafin/master

Modified SID settings to allow up to 10k coverage and lowered AF thresho...
Fixes for nglims-based sample preparation: correctly specify upload directory for Galaxy, handle controls, and avoid passing empty fastq files through
Improvements for Galaxy upload: handle creation of missing Galaxy database libraries, support nglims-based specifications, avoid uploading indexes