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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
Added option to remove all ambiguous SNPs
Added option to change the reference allele of the input data to match reference allele of the reference data set.
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.
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.
Better handling of variants without a mapping.
Fixed problems with TriTyper writer when performing both sample filter as alignment in a single run.
Added better error messages in case all samples or variants are removed by the filters.
Added MACH R2 Measure to filter the input data.
Some very minor improvements
New much faster VCF reader, fixed bug combining sample filter and MAF filter, improved logging of excluded and swapped SNPs
Added support for reading and writing TriTyper data. Added variant and sample filters for input data.
Fixed minor bug causing vcf.gz files not to be automatically recognized as a VCF file
Added support for reading and writing oxford gen data.
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/
- QTL mapping pipeline
- Genotype Harmonizer
- Genotype IO
- ASE
- GADO Command line
- Downstreamer
- GeneNetwork Analysis
Analysis plans
Other