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Commits on Jan 20, 2015
  1. @chapmanb
Commits on Jan 18, 2015
  1. @chapmanb

    Provide additional exposure of non-affected samples in plots and auto…

    chapmanb authored
    …matically generate BED file with regions in plot
Commits on Jan 16, 2015
  1. @chapmanb

    Avoid filtering unaffected CNV/SV calls when preparing summary to pro…

    chapmanb authored
    …vide better background of calls in unaffected samples
Commits on Jan 13, 2015
  1. @chapmanb

    Improve summarization of structural variant results: use risk factors…

    chapmanb authored
    … calculated by Rory and do a better job of eliminating false positives
  2. @chapmanb

    Improved summarization of structural variants: combine by batches fir…

    chapmanb authored
    …st, then filter, then feed into the global plotting and view. Sort plots by abundance within families. Provide detailed breakdowns of calls per region.
Commits on Jan 9, 2015
  1. @chapmanb
Commits on Jan 8, 2015
  1. @chapmanb

    Summarize and plot structural variant calls across multiple families,…

    chapmanb authored
    … visualizing shared events in cases and not controls
Commits on Dec 27, 2014
  1. @chapmanb
Commits on Dec 25, 2014
  1. @chapmanb
Commits on Jun 18, 2014
  1. @chapmanb
Commits on Jun 17, 2014
  1. @chapmanb
Commits on May 4, 2014
  1. @chapmanb
  2. @chapmanb

    Script for compressing existing BAM files to CRAM for storage improve…

    chapmanb authored
    …ments. Update for squaring script
Commits on Apr 9, 2014
  1. @chapmanb

    Scripts for running priority 1 and 2 squaring off; preparing SV calls…

    chapmanb authored
    … for pilot and update variant calling configuration
Commits on Apr 4, 2014
  1. @chapmanb
Commits on Jan 17, 2014
  1. @chapmanb

    Update illumina prep and run prep scripts to generalize to Sanger/Ody…

    chapmanb authored
    …ssey; handle new bcbio-nextgen parallelization; incorporate bcbio.nextgen.recall into workflow
Commits on Dec 22, 2013
  1. @chapmanb
Commits on Dec 20, 2013
  1. @chapmanb

    Move to cleaned data setup on Odyssey. Avoid structural variant call …

    chapmanb authored
    …inclusion in VCF since they break downstream merging tools
Commits on Dec 11, 2013
  1. @chapmanb
Commits on Dec 4, 2013
  1. @chapmanb

    Include support for gender in Alz samples and prepare configuration f…

    chapmanb authored
    …or latest family of interest
Commits on Dec 1, 2013
  1. @chapmanb

    Update configuration preparation to use template functionality with C…

    chapmanb authored
    …SV metadata. Include new family of interest in configuration file
Commits on Nov 26, 2013
  1. @chapmanb
  2. @chapmanb

    Provide java main class to enable easier access to snp-assess functio…

    chapmanb authored
    …nality through pre-build jars
Commits on Nov 25, 2013
  1. @chapmanb
  2. @chapmanb
  3. @chapmanb

    Start of reproducible script to handle data retrieval, code installat…

    chapmanb authored
    …ion and pipeline running for HIV paper
Commits on Nov 21, 2013
  1. @chapmanb
Commits on Nov 4, 2013
  1. @chapmanb
  2. @chapmanb

    Provide more general splitting of priority variants. Handle multiple …

    chapmanb authored
    …machine setups cleanly in configuration file
Commits on Oct 30, 2013
  1. @chapmanb

    Generalize run prep configuration file to handle new priority samples…

    chapmanb authored
    …. Clean up PED file post-loading for new gemini structure
Commits on Sep 23, 2013
  1. @chapmanb
Commits on Sep 16, 2013
  1. @chapmanb
Commits on Aug 31, 2013
  1. @chapmanb

    Generalize plotting functionality for sample regional coverage and pr…

    chapmanb authored
    …ovide boxplots for in-depth investigation of coverage in specific genomic regions
Commits on Aug 25, 2013
  1. @chapmanb
  2. @chapmanb

    Finalize coverage per gene per sample plot: summarize with a single n…

    chapmanb authored
    …umber using area under cumulative distribution function, clean up plot axes and labels
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