Ensemble enabled for tumor-normal studies.
Enable streaming S3 input to RNA-seq and variant processing.
Fixes for GATK joint haplotype calling: correctly batch groups when using post-alignment preparation, provide useful error message when missing batches, filter stray NON_REF gVCF calls in GATK HaplotypeCaller output. Thanks to @lpantano
Update working with RNA-seq pipeline instructions
Fix data grabbing script to have a consistent name
Remove LCR regions before feeding into scalpel to improve runtimes on whole genome analyses
Merge pull request #562 from mjafin/somatic_ensemble

Ensemble enabled for tumor-normal studies
Update cn_mops.py

Proposing these changes as I've seen errors coming from the (experimental) ``calcFractionalCopyNumbers`` function but same analyses finish fine using ``calcIntegerCopyNumbers``.
If upgrading to development version, also upgrade the tools.
Add script to get data from the SEQC project.
Fix name of SEQC data grabber script.
 add a for loop.
Merge pull request #565 from kern3020/master

Simplified RNA get data script a bit
Enable detection of sample mixups with 'mixup_check' input parameter. Enable for standard and variant calling pipelines. Ensure correct handling of integer batch names
Improve BED preparation by moving creation of merged BED files to initial steps. Avoids potential race conditions when processing the same file in parallel over multiple chromosomes during initial runs
Fix VarScan header output to be compatible with other callers. Enables usage of VarScan in ensemble calling
Merge pull request #564 from mjafin/patch-4

Update cn_mops.py
Enable passing command line arguments to GATK HaplotypeCaller. Thanks to Severine Catreux
Strip UCSC browser commands from input BED files during preparation. Fixes #566
SNAP aligner: use streaming de-duplication and sorting with samblaster and sambamba