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Commits on Nov 2, 2015
Commits on Jul 17, 2015
  1. v0.2.6: Really avoid removing reference calls when using sort-vcf on …

    committed Jul 17, 2015
    …structural variant calls. Thanks to @mjafin
Commits on Jul 16, 2015
  1. v0.2.5: support for GRCh38 and better variant sorting

    committed Jul 16, 2015
    - Do not remove reference calls or do any chromosome renaming when sorting
      by position with `variant-utils sort-vcf`.
    - Add support for GRCh38 by avoiding issues with large numbers of contigs.
    - Add ability to only fix sample name in input VCF without doing a full prep.
Commits on Mar 25, 2015
  1. Update download link for v0.2.4

    committed Mar 25, 2015
  2. v0.2.4: De-prioritize multi-allele calls where PL and AD values do no…

    committed Mar 25, 2015
    …t match a final, non-multiallelic ensemble call. Thanks to Shalabh Suman
Commits on Feb 1, 2015
Commits on Jan 15, 2015
Commits on Jan 9, 2015
  1. Ensemble calling: correctly handle inputs with same base filename in …

    committed Jan 9, 2015
    …different directories. Fixes #23
Commits on Jan 3, 2015
  1. v0.2.1: Avoid normalization as part of ensemble process, which can ca…

    committed Jan 3, 2015
    …use issues with some inputs (Fixes #21). Instead rely on upstream normalization
Commits on Dec 18, 2014
  1. v0.2.0: Avoid putting fully specified indels into structural variant …

    committed Dec 17, 2014
    …comparison, which can lead to masked smaller calls on heterozygous deletions. Thanks to Severine Catreux
Commits on Nov 7, 2014
  1. v0.1.9: Fix issues dealing with complex input samples. Handle inputs …

    committed Nov 6, 2014
    …with identical file names. Thanks to Severine Catreux. Resort multisample inputs that have inconsistent sample orders. Fixes chapmanb/bcbio-nextgen#653
Commits on Oct 30, 2014
  1. v0.1.8: Prevent swapped headers/samples during prep in cases where mu…

    committed Oct 29, 2014
    …lti-sample input files have not previously been through GATK. The GATK LeftAlign steps re-sort the samples and this header was not being correctly passed to the next step. Fixes #19
Commits on Sep 7, 2014
Commits on Aug 21, 2014
  1. Nove to using GATK 3.2 with new htsjdk namespace and lots of import c…

    committed Aug 21, 2014
    …hanges. Enables Java 8 support
Commits on Jul 23, 2014
Commits on May 28, 2014
  1. Ensure posterior likelihoods are consistent with alleles when creatin…

    committed May 28, 2014
    …g new genotypes from ensemble calls. Removes PLs when not matching combined calls. Fixes #16
Commits on May 24, 2014
  1. Update sort-vcf variant-utils to handle new prep-vcf function and ena…

    committed May 24, 2014
    …ble sorting by reference position
Commits on May 18, 2014
  1. Avoid trying to re-align and normalize very long indels which cause c…

    committed May 18, 2014
    …ause null pointer errors. These are dealt with by structural variation comparions. Thanks to Severine Catreux
Commits on Apr 28, 2014
  1. v0.1.6 release

    committed Apr 28, 2014
Commits on Apr 26, 2014
  1. Provide comparetwo functionality to provide concordance/discordance f…

    committed Apr 26, 2014
    …or pair of variants within defined regions
Commits on Apr 10, 2014
Commits on Apr 8, 2014
  1. Merge pull request #15 from tzhughes/patch-1

    committed Apr 8, 2014
    Small correction to doc for vcfSimpleStatsWalker
Commits on Apr 7, 2014
  1. @tzhughes

    Small correction to doc for vcfSimpleStatsWalker

    tzhughes committed Apr 7, 2014
    Hope it is ok to just put this straight here.
Commits on Apr 6, 2014
  1. Include evaluation calls instead of reference calls in concordant out…

    committed Apr 6, 2014
    …put. Thanks to Severine Catreux
Commits on Mar 26, 2014
  1. Resolve ensemble calling issues: ensure input VCFs have consistent sa…

    committed Mar 25, 2014
    …mple headers and correctly prioritize reads with depth genotype annotations. Thanks to Shalabh Suman
Commits on Mar 15, 2014
  1. v0.1.5: Finalize variant evaluation support with new bcbio-nextgen ch…

    committed Mar 15, 2014
    …anges: handle bgzip inputs, support non-GATK callable regions, avoid VariantEval due to java errors. Thanks to Severine Catreux.
Commits on Mar 13, 2014
Commits on Mar 8, 2014
Commits on Mar 5, 2014
  1. v0.1.4

    committed Mar 5, 2014
Commits on Mar 3, 2014
  1. Handle bgzipped inputs to validation, using non-indexed retrieval to …

    committed Mar 3, 2014
    …get headers from VCF file. Remove need for ref-file when retrieving VCF iterators.
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