fixed typo
Re-work de-duplication to occur streaming with alignment. Uses samblaster/biobambam to handle de-duplication, avoiding need for BAM preparation step in cases with no realignment and recalibration.
Documentation: Add wget to required software for installation. Thanks to Tim Hughes. Add pointers to downstream analysis tools, thanks to @lbeltrame #195
Add module for streaming de-duplication integrated with alignment
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Merge discordant and split read pairs from alignment parts when using samblaster. Avoid needing to re-run analysis during lumpy SV calling
Perform regional splitting of samples grouped by batches instead of globally. Enables more complex sample input setups.
Add slides from ABCD talk. Clean up talk list and add link to images for reuse
Handle avoiding low complexity subsets on regions if supplied as tuple instead of BED file
Update outputs.rst

another way to visualize coverage for targeted NGS (exome) experiments
Update outputs.rst
Provide ability to specify a global temporary directory in resources. Helps avoid shared filesystem IO when large local /scratch disk is present on machines. Fixes #399
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Merge pull request #402 from tanglingfung/patch-2

Update outputs.rst
Avoid VCF concatenation errors when first input file is empty. Thanks to Jiantao Shi.
Provide useful error messages if sample info YAML is missing or not supplied, removing old functionality of fetching directly from Galaxy
Additional cleanup of edge cases for splitting and merging samples: no-overlap inputs, cancer tumor/normal, bamprep inputs. Fixes #400 Fixes #378
Clean delly output GLs to enable compatibility with GATK
Galaxy upload: Provide upload of QC results via conversion to pdf. Fixes for Galaxy upload: add permissions for creating folders by name and handling bgzipped VCF inputs
add ngscat to downstream analysis

another tool to assess the efficiency of targeted enrichment sequencing