LDhelmet

Fine-scale recombination rate estimation.

Brought to you by: andrewhc, j3nk1ns, yssong

Last Update: 2021-06-23

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NOTE: This project has migrated to GitHub: https://github.com/popgenmethods/LDhelmet

LDhelmet performs statistical inference for fine-scale variable recombination rate estimation. The source code and the recombination maps for two populations of Drosophila melanogaster are available for download.

Reference:
Andrew H. Chan, Paul A. Jenkins, Yun S. Song (2012). Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster. PLoS Genet 8(12): e1003090. doi:10.1371/journal.pgen.1003090

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2012-05-02

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inGAP-family
inGAP-family provides an efficient and effective framework to discover, filter and visualize DNA polymorphisms and structural variants from alignment of short reads. Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for detection of polymorphisms and structural variants, and for further evaluation of predicted variants and identification of mutations related to genotypes. inGAP-family is implemented in Java to provide a platform-independent tool, and to support both command line mode and graphical mode. The output could also be visualized in user-friendly graphical interface for checking SNPs, indels and large-scale structural variants.