Improve documentation on AWS SLURM and add details about running monitoring graphs locally
Initial framework for variant prioritization to use in tumor-only calling. Create GEMINI database of tumor-only calls to use for retrieval of external metadata for each variant.
Explicitly log in UTC and use iso8601 time output. Fixes chapmanb/bcbio-nextgen-vm#46
Allow mixing joint and batched calling in a single configuration. Fixes for uploading joint called results. Thanks to Zhengqiu Cai
Framework for variant prioritization and filtering based on external annotations: provide full annotating and filtering based on external data
Document naming restrictions for S3 buckets and simple interactions through SSL
Ensure remote S3 files are correctly bgzipped when converting from illumina quality format. Thanks to Yuri
Ensure problem Lumpy calls cleaned prior to sorting to ensure valid VCF goes into GATK/bcbio.variation post processing. Fixes #678
Initial tumor-only prioritization approach: filter calls found in global populations, prioritize calls in known cancer databases and with high impact changes
Update tumor-paired cancer template
Avoid loading snpEff databases when not needed for downstream analysis. Improved RNA-seq and VEP-only analyses
Do not use extra gunzip when file input fed through seqtk for conversion from illumina to standard quality values. Fixes #699
Handle edge cases in calculating frequency for prioritization and do not pull in as many positives with COSMIC/Clinvar support by excluding those with multiple negative sources
add strandness to express

rm tmp dir
Merge branch 'master' of github.com:/lpantano/bcbio-nextgen