HaploVar
Defining Local Haplotype Variants for Use in Trait Association and Trait Prediction Analyses
Description
A local haplotyping tool for use in trait association and trait prediction analyses pipelines. 'HaploVar' enables users take single nucleotide polymorphisms (SNPs) (in VCF format) and a linkage disequilibrium (LD) matrix, calculate local haplotypes and format the output to be compatible with a wide range of trait association and trait prediction tools. The local haplotypes are calculated from the LD matrix using a clustering algorithm called density-based spatial clustering of applications with noise ('DBSCAN') (Ester et al., 1996) <ISBN: 1577350049>.
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |