Update GATK dependency to 2.5-2, using only the MIT licensed framework code. Add in used walkers and annotators from GATK 2.3 lite
Build fai FASTA indexes with samtools if not present: equivalent java functionality removed from GATK and Picard
Comment out merging test relying on GATK UnifiedGenotyper for recalling
Remove automation for GATK variant quality recalibration based filtering, which is no longer supported in GATK 2.5 framework
Generalize VCF parsing to variant contexts to remove dependency on GATK and use new Tribble/Picard components
Remove use of UnifiedGenotyper for genotyper recalling to leave clean dependency on only MIT licensed portion of GATK codebase
Work towards a cleaner core with associated utilities to reduce dependencies. Update remote dependencies to latest versions
Include additional libraries required for GATK commandline processing into slimmed down requirements
v0.0.9 release
Include Illumina structural variant calls as part of Illumina to GATK compatible converge and merge.
Write prepped illumina output files to non-project directory to treat Illumina inputs as read-only
Cleanup of VCF precleaning normalize code to improve performace by avoiding unnecessary lookups
Cleanly handle missing chromosomes we know about when mapping hg19 to GRCh37 with an alternative genome reference supplied
Improve interaction with gemini: handle cases with partially broken gemini installs and avoid multiple callouts to check for gemini when retrieving variant attributes
Fix for api testing when gemini not present
Correctly fill in missing reference bases for indels padded with Ns
Allow specifying temporary working directories for variant prep, to allow processing on local /scratch space
Framework for rapid comparisons of variant calls to genotype VCFs. Useful for first pass sample sanity checks
Provide summary file comparing multiple variants against a base VCF with multiple samples. Handles the case of Illumina output against an array set of known calls
Provide parallelization of quickcompare over multiple cores using Clojure reducers