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Commits on May 23, 2012

• Support latest version of GATK report output

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Commits on May 16, 2012

• Use Freebayes parameters in use for 1000 genomes calling

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Commits on May 13, 2012

• Allow password and token-based login. Allow relative paths passed into download.

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• Clean up API: avoid multiple user/password references to more easily support single sign on tokens

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Commits on May 11, 2012

• Support custom derived masked genomes with snpEff

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• Small example of using GenomeSpace API from Clojure

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• Handle empty variant_regions with separately specified split region when genotyping with Freebayes

  chapmanb

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• Handle interval specifications for region and BED file where GATK does not detect an overlap

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Commits on May 10, 2012

• Delay starting of manager and cluster works so time based managers will schedule manager first

  chapmanb

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Commits on May 9, 2012

• Correctly sort existing split FASTQ files to match split numbering

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• Allow specification of cores on commandline for local running of pipeline

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Commits on May 8, 2012

• Allow targetted variant calling. Use BED file to limit recalibration, realignment, variant calling and annotation

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Commits on May 7, 2012

• Documentation for alignment FASTQ splitting.

  chapmanb

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• Support splitting of input FASTQ files to parallelize alignment. Remove duplicates by default to handle non-GATK variant calling pipelines.

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Commits on May 2, 2012

• Additional support for supplying VCF background files

  chapmanb

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• Support haploid calling, background VCF input and specific target regions as part of freebayes variant calling

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Commits on Apr 30, 2012

• Merge branch 'master' of github.com:chapmanb/bcbb

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• Update query example to match paper text

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Commits on Apr 20, 2012

• Handle new location file format for OLB 1.9

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Commits on Apr 18, 2012

• Merge branch 'master' of github.com:chapmanb/bcbb

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• Initial framework for converting Complete Genomics structural variant events to VCF

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Commits on Apr 3, 2012

• Merge pull request #56 from vals/brads-master

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Commits on Apr 2, 2012

• Made a helper function that tries doing float conversion

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Commits on Mar 29, 2012

• Support detection of tandem duplications and translocation events, annotating in VCF appropriately

  chapmanb

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Commits on Mar 28, 2012

• Detect paired sets of breakend reads for more complex events. Convert inversions into reduced VCF representation

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• Collapse hydra identified deletions into standard VCF representation

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• Add ability to filter Hydra VCF output by read support

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• Update Hydra BEDPE to VCF breakpoint conversion. Correctly handle all breakend orientation cases.

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Commits on Mar 23, 2012

• Revert bowtie2 change since -M only reports best alignment

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• Report single alignment from bowtie2 to match bwa approach

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Commits on Mar 20, 2012

• Avoid adding extra Illumina base when bc_offset used. Thanks to Yan Wang and Mark Borowsky.

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Commits on Mar 19, 2012

• Generalize sanitization of text strings for LaTeX

  chapmanb

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Commits on Mar 16, 2012

• Update dbSNP and Mills standard indels for latest GATK

  chapmanb

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• Remove no phone home flag for GATK to be compatible with GATK 1.5

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• Example hydra converted VCF output

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