Genotype Harmonizer Download - molgenis/systemsgenetics GitHub Wiki

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

Version 1.4.28 (09-12-2024)

Improved speed of bgen writer and bug fix in logging.

• GenotypeHarmonizer-1.4.28-dist.zip
• GenotypeHarmonizer-1.4.28-dist.tar.gz

Version 1.4.25 (29-10-2022)

Fixed problem with build of the binaries.

• GenotypeHarmonizer-1.4.25-dist.zip
• GenotypeHarmonizer-1.4.25-dist.tar.gz

Version 1.4.24 (24-10-2022)

Minor bug fix

• GenotypeHarmonizer-1.4.24-dist.zip
• GenotypeHarmonizer-1.4.24-dist.tar.gz

Version 1.4.23 (08-01-2020)

Added reading and writing support for binary gen format

• GenotypeHarmonizer-1.4.23-dist.zip
• GenotypeHarmonizer-1.4.23-dist.tar.gz

Version 1.4.20 (19-05-2017)

Added option to remove all ambiguous SNPs

• GenotypeHarmonizer-1.4.20-dist.zip
• GenotypeHarmonizer-1.4.20-dist.tar.gz

Version 1.4.18 (08-09-2016)

Added option to change the reference allele of the input data to match reference allele of the reference data set.

• GenotypeHarmonizer-1.4.18-dist.zip
• GenotypeHarmonizer-1.4.18-dist.tar.gz

Version 1.4.17 (26-07-2016)

Several small fixes to Genotype Harmonizer and Genotype IO. Most notably: TRITYPER files can now include non-SNP alleles, such as amino-acids or indels. These alleles are recoded to A/C SNPs, reference will be represented as A. Small fix in variant renaming when harmonizing SNP-names to match a reference panel.

• GenotypeHarmonizer-1.4.17-dist.zip
• GenotypeHarmonizer-1.4.17-dist.tar.gz

Version 1.4.15 (12-06-2015)

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-1.4.15-dist.zip
• GenotypeHarmonizer-1.4.15-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/