Document design descisions and approaches #48 #49 #50
Extract VCF concatenation to allow more lightweight implementation that avoids GATK when only merging intervals. Only framework in place so far, not implementation
Be more explicit about use of VQSR and avoid usage in regional, exome and low coverage cases. It has bad performance characteristics when run on low coverage whole genomes
Improve logic for selecting bwa mem versus bwa align to handle trimming. Use bwa mem when more than half of first 500 reads are longer than threshold of 75. Fixes #50
Add MIT license to top level directory. Thanks to @lbeltrame. #54
STAR support added.
First pass at new approach installer: bootstraps a local python installation using anaconda, then use CloudBioLinux deploy functionality to install data and tools. Allows updatable tools and data from within install application
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Clarity edit.
Clarity edit.
Fix for finding RNA-SeQC .jar file.
Added rna-seqc to the test configuration file.
whitespace fixes
Added provenance tracking.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added htseq-count to output files named as the sample name.
Merge branch 'htseq-fix-wip'
Put htseq-count files into their own directory.
Concatenate variant files split by regions using a simplified approach that avoids GATK overhead and file locking issues. Requires sorting files by region then simple concat in order
Additional updates to in-development installation process: Bug fixes, better progress reporting and write output system YAML files