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0.2.6 (17 Sep 2019)

  • Fix problem with not converting alleles to strings during v0.2.5 update.

0.2.5 (1 Sep 2019)

  • Handle input VCFs with differing cases in REF and ALT alleles.

0.2.4 (22 Feb 2019)

  • Fix platypus calling to correctly add contig headers to avoid GATK4 GatherVcf errors.

0.2.3 (12 Feb 2019)

  • Fix wrapper script to avoid java in /bin/java without JAVA_HOME set.

0.2.2 (1 Feb 2019)

  • Handle input to bcftools concat when all original files have no variants.
  • Remove problematic INFO and FORMAT fields for FreeBayes. In complex decomposed, it retains more AD/AO/QA/GL fields then the headers allow, causing bcftools failures.
  • Fix logging to correctly raise errors on failures.

0.2.1 (17 Jan 2019)

  • Clarify filters on depth (DP) which fail on recent bcftools when present in both INFO and FORMAT key/values.

0.1.9 (3 August 2018)

  • Remove usage of gatk-framework, which is no longer included in bcbio. Replace GATK usage with bcftools merge and concat.

0.1.8 (18 May 2018)

  • Fix tabix index error for variants present at position 1 of contigs.

0.1.7 (15 August 2016)

  • Avoid FreeBayes error when running --variant-input without an empty VCF.

0.1.6 (25 April 2016)

  • Handle larger merge sizes with additional memory specifications up to 3000 or more samples.
  • Use local temporary directories for GATK calls, avoiding filling up temporary space. Thanks to Roman Valls Guimerà.
  • Correctly parse sample names from large numbers of inputs without causing overflow error.
  • Do not silently exit if running into Java memory errors.
  • Automatically convert ensemble output files to bgzipped output.

0.1.5 (15 April 2016)

  • Add genotype qualities (GQ) to output of FreeBayes recalls.
  • Use samtools instead of scramble for CRAM integration.

0.1.4 (15 October 2015)

  • Annotate ensemble variant calls with names of callers supporting an ensemble variant.

0.1.3 (13 October 2015)

  • Support latest GATK and htsjdk to handle issues with gVCFs on GATK 3.4 and different command line options in gatk-framework.

0.1.2 (25 April 2015)

  • Correctly handle copies of single files in transactional directories.

0.1.1 (15 April 2015)

  • Correctly intersect files when one of the inputs is empty. Thanks to Daryl Waggott.

0.1.0 (7 April 2015)

  • Fix command line sorting issues with X/Y chromosomes. Thanks to Lorena Pantano.
  • Separate command line help library into bcbio.run for use outside of bcbio.variation.recall.

0.0.9 (2 April 2015)

  • FreeBayes: update with options for latest validated version 0.9.21-7

0.0.8 (20 March 2015)

  • Avoid copy errors when merging recalls with only a single region.

0.0.7 (23 February 2015)

  • Fix errors encountered on large runs, adding additional temporary directory usage during copy and spit commands to prevent partial files.

0.0.6 (30 January 2015)

  • Correctly handle identically named input files for recalling.
  • Avoid filtering low quality reference calls when recalling with Platypus.
  • Correctly support vcffixup stdin in recent vcflib.
  • Support new sambamba index changes.

0.0.5 (1 December 2014)

  • Ensemble calling: handle variant inputs with multiple identical calls.

0.0.4 (28 October 2014)

  • FreeBayes recalling fixes to support GATK compatibility: remove duplicate alternative alleles and ceil very low FreeBayes quality scores.

0.0.3 (26 October 2014)

  • Fix FreeBayes recalling/squaring off to better distinguish reference and no call. Avoid filtering low-quality reference positions and assigning as no call while still removing problem variants.
  • Fix ensemble calling for cases with closely spaced variants containing identical ref/alts.

0.0.2 (29 September 2014)

  • Initial implementation of intersection based ensemble calling. Handle germline and tumor/normal cases.
  • Use new picard and htsjdk libraries for variant manipulation.

0.0.1 (20 September 2014)

  • Initial release with support for parallel genome merging and squaring off/joint calling with FreeBayes, Platypus and samtools.