First draft of Scalpel integration
First draft of Scalpel integration
Merge branch 'scalpel' of https://github.com/mjafin/bcbio-nextgen into scalpel
mutect.py and scalpel.py bug fixes for integration with bcbio
mutect.py small fix to assume two separate callers always used
First draft of Scalpel integration
mutect.py and scalpel.py bug fixes for integration with bcbio
mutect.py small fix to assume two separate callers always used
Merge branch 'scalpel' of https://github.com/mjafin/bcbio-nextgen into scalpel
Default filter value REJECT for common variants in scalpel paired mode calling
Default to scalpel for indels in mutect.py if not using Appistry mutect
Trailing white spaces removed
Merge branch 'master' into scalpel
Use local temporary directories for pybedtools tempfiles. Avoids scaling issues with filling up global temporary space and allows use of configured high speed temporary storage
Added standalone support for Scalpel calling
Move callable region calculation to use bedtools with groupby thanks to tips from @arq5x. Provides improved speed and memory usage over pysam based implementation. Fixes for pybedtools temp directory specification
Ensure pybedtools temporary directory sets occur before multiprocessing to avoid thread conflicts. Clean up temporary directory setting in context manager to enable reverts following processing
Correctly handle preparing coverage regions for whole chromosomes without variant sub-regions, by saving ref bedtool after creation
Merge pull request #432 from mjafin/scalpel

Scalpel
Fix edge cases for updated callable calculation: contigs with no mapped reads and high coverage regions