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Commits on Jun 24, 2016
Commits on Jun 17, 2016
  1. Use GiaB 3.2.2 calls for NA24385/NA12878 truth set

    Improve truth set using better consolidated NA24385 calls from the
    latest Genome in a Bottle release.
    chapmanb committed Jun 17, 2016
Commits on Mar 26, 2016
Commits on Mar 22, 2016
Commits on Mar 21, 2016
Commits on Mar 17, 2016
  1. Document approach and provide link to truth set. Include removal of c…

    …onsistent false positives in truth set preparation
    chapmanb committed Mar 17, 2016
Commits on Mar 13, 2016
Commits on Mar 12, 2016
  1. Improve preparation of Genome in a Bottle truthset

    - Add complete genomic callset when creating NA24385 calls for NA12878
      mixture.
    - Allow somatic comparison with created truthset
    - Avoid converting to hg19 naming for contigs
    chapmanb committed Mar 12, 2016
Commits on Feb 29, 2016
Commits on Feb 22, 2016
Commits on Feb 21, 2016
Commits on Jan 29, 2016
Commits on Jan 20, 2016
Commits on Jan 17, 2016
  1. Improve preparation for NA12878/NA24385 mixture truth set

    Homozygous calls get converted into heterozygotes since the mixture
    results in these no longer being homozygous. If we look at frequencies
    longer term could adjust these smartly to represent expected freqs.
    chapmanb committed Jan 17, 2016
Commits on Jan 14, 2016
Commits on Jan 11, 2016
Commits on Jun 23, 2015
Commits on Jun 22, 2015
Commits on Jun 20, 2015
Commits on Jan 20, 2015
Commits on Jan 18, 2015
  1. Provide additional exposure of non-affected samples in plots and auto…

    …matically generate BED file with regions in plot
    chapmanb committed Jan 18, 2015
Commits on Jan 16, 2015
  1. Avoid filtering unaffected CNV/SV calls when preparing summary to pro…

    …vide better background of calls in unaffected samples
    chapmanb committed Jan 16, 2015
Commits on Jan 13, 2015
  1. Improve summarization of structural variant results: use risk factors…

    … calculated by Rory and do a better job of eliminating false positives
    chapmanb committed Jan 13, 2015
  2. Improved summarization of structural variants: combine by batches fir…

    …st, then filter, then feed into the global plotting and view. Sort plots by abundance within families. Provide detailed breakdowns of calls per region.
    chapmanb committed Jan 13, 2015
Commits on Jan 9, 2015
Commits on Jan 8, 2015
  1. Summarize and plot structural variant calls across multiple families,…

    … visualizing shared events in cases and not controls
    chapmanb committed Jan 8, 2015
Commits on Dec 27, 2014
Commits on Dec 25, 2014
Commits on Jun 18, 2014
Commits on Jun 17, 2014
Commits on May 4, 2014
  1. Script for compressing existing BAM files to CRAM for storage improve…

    …ments. Update for squaring script
    chapmanb committed May 4, 2014
Commits on Apr 9, 2014
  1. Scripts for running priority 1 and 2 squaring off; preparing SV calls…

    … for pilot and update variant calling configuration
    chapmanb committed Apr 9, 2014
Commits on Apr 4, 2014