Provide hard filtering for indels when initial VQSR fails only on indels
Merge
Fix bug in test_pipeline.py relating to change in programs._get_versions() name
Merge pull request #7 from mariogiov/fix_test_pipeline

Fix bug in test_pipeline.py relating to change in programs._get_versions...
Merge pull request #99 from mariogiov/fix_test_pipeline

Fix bug in test_pipeline.py relating to change in programs._get_versions...
Merge pull request #8 from chapmanb/master

Merge from Brad upstream
Changed pipeline/config_utils.py to expand shell variables into paths (specifically for snpEff)
Merge branch 'bcbio_variation_expand_snpeff_path' into bcbio-devel