v1.5.1

This release increases the amount of RAM allocated to the IndelRealigner step. It also skips separating the sample VCF file into separate SNP and INDEL VCF files unless variant quality score recalibration is performed.

v1.5.0

This release adds variant evaluation to the raw variants called by the Haplotype caller, and fixes a bug which meant that the separate INDEL file was not evaluated at all.

v1.4.0

The release notes for this release are available here: https://github.com/NationalGenomicsInfrastructure/piper/releases/tag/v1.4.0 This release "re-tags" 70eb84f to allow Zenodo to create a doi for the release.

v1.4.0

Major changes:

• If given a GATK stand-alone license on the command line, the phone home feature of GATK will be disabled
• Introduced a command-line argument to set how qualimap will treat duplicate reads. Default is to use the duplicates marked by picard.
• Improved build process to include the option to create deployable zip-files
• Removed bundling of sbt version, which means tests depending on the testNG have been disabled.

v1.3.0

Major changes

• VCF files are compressed (with GATK) by default
• Option to include/exclude OQ, BD and BI tags during bam recalibration
• Option to remove recalibrated bam from final output
• Fixes to processing BAMs when splitting using ParallelShell
• Increase RAM allocated to qualimap

Minor changes

• Include the snpEff reference version in version_report.txt
• Fixed calls to snpEff (RAM, skip intermediate files, compress output)
• Fixes to handling intermediate files and some un-annotated output files (mostly index files)

v1.2.0-beta2

Please note that this is not a stable release!

Major changes

• DNABestPracticeVariantCalling now accepts a xml file which configures the paths to programs and resource files. However all of these paths can also be overriden from the command line if you wish to do so. This approach will be added to all other workflows further down the line, but right now the focus is on getting the DNABestPracticeVariantCalling up to speed to the Swedish Genomes project.

Minor changes

• Better setup instructions.

v1.2.0-beta1

Major changes

• Changes to adopt Piper to running on the Milou cluster.
• All QScripts now get their settings from the setup xml.
• All the different DNA best practice scripts merged to a single QScript - making the process of running in much smoother, as well as simplifying future development considerably.

Minor changes

• Option to only run alignments in Haloplex workflow.
• Haloplex scripts will do a simple conversion of input files to run on b37 human reference instead of hg19.
• Adding some simple example scripts for demo purposes (to support the Piper workshop).
• ReportParser app added - a simple application to parse report files and extract the number of libraries sequenced and reads passed filter for a sample.
• Improvements to the documentation
• A lot of minor fixes.