Genotype Harmonizer Download

The Genotype Harmonizer releases can be downloaded below. On the bottom of the page there is also a link to the latest snap-shot version. Usage information can be found [here](Genotype Harmonizer)

Version 1.4.13 (03-06-2015)

Writing to Plink formats will give proper numbering to sex chromosomes. Alignment will not automatically exclude variants with MAF = 0. Converting to TriTyper will recode indels as SNPs so they do need to be excluded. Some background improvements to the used [Genotype-IO] API.

• GenotypeHarmonizer-1.4.13-dist.zip
• GenotypeHarmonizer-1.4.13-dist.tar.gz

Version 1.4.9 (07-10-2014)

Better handling of variants without a mapping.

Fixed problems with TriTyper writer when performing both sample filter as alignment in a single run.

• GenotypeHarmonizer-1.4.9-dist.zip
• GenotypeHarmonizer-1.4.9-dist.tar.gz

Version 1.4.7 (03-10-2014)

Added better error messages in case all samples or variants are removed by the filters.

• GenotypeHarmonizer-1.4.7-dist.zip
• GenotypeHarmonizer-1.4.7-dist.tar.gz

Version 1.4.6 (12-09-2014)

Added MACH R2 Measure to filter the input data.

• GenotypeHarmonizer-1.4.6-dist.zip
• GenotypeHarmonizer-1.4.6-dist.tar.gz

Version 1.4.5 (28-08-2014)

Some very minor improvements

• GenotypeHarmonizer-1.4.5-dist.zip
• GenotypeHarmonizer-1.4.5-dist.tar.gz

Version 1.4.1 (18-06-2014)

New much faster VCF reader, fixed bug combining sample filter and MAF filter, improved logging of excluded and swapped SNPs

• GenotypeHarmonizer-1.4.1-dist.zip
• GenotypeHarmonizer-1.4.1-dist.tar.gz

Version 1.3.4 (18-03-2014)

Added support for reading and writing TriTyper data. Added variant and sample filters for input data.

• GenotypeHarmonizer-1.3.4-dist.zip
• GenotypeHarmonizer-1.3.4-dist.tar.gz

Version 1.3.1 (23-10-2013)

Fixed minor bug causing vcf.gz files not to be automatically recognized as a VCF file

• GenotypeHarmonizer-1.3.1-dist.zip
• GenotypeHarmonizer-1.3.1-dist.tar.gz

Version 1.3.0

Added support for reading and writing oxford gen data.

• GenotypeHarmonizer-1.3.0-dist.zip
• GenotypeHarmonizer-1.3.0-dist.tar.gz

Version 1.2.3

• GenotypeHarmonizer-1.2.3-dist.zip
• GenotypeHarmonizer-1.2.3-dist.tar.gz

Last automatic build

The last automatic build based on the current code-base can be downloaded here: http://www.molgenis.org/jenkins/job/systemsgenetics/nl.systemsgenetics$Genotype-Harmonizer/lastBuild/