Haplotype frequency estimation software tools | Pool sequencing data analysis
A variety of hypotheses have been proposed for finding the missing heritability of complex diseases in genome-wide association studies. Studies have focused on the value of haplotype to improve the power of detecting associations with disease. To facilitate haplotype-based association analysis, it is necessary to accurately estimate haplotype frequencies of pooled samples.
Considers disjoint pools of unrelated individuals to deduce haplotype frequencies. Haplopool is an application leaning on a selection of the maximum-likelihood haplotype configuration for each pool from estimated frequencies. It provides a method able to deal with missing data and genotyping error. This software can also be employed to phase traditional genotype data.
Taking advantage of prior haplotype information contained in the database, it infers haplotype frequencies from pooled sequencing data. It is open source and available for download and can be easily integrated into existing analysis pipelines.
Assists users in family-based next-generation sequencing (NGS) analysis for disease studies. FamPipe is a pipeline which can be applied to the analysis of Mendelian disorders or complex diseases. Two family-based imputation tools (Merlin and GIGI) are integrated for imputation analysis when the data consist of both sequencing and single nucleotide polymorphism (SNP) array data.
Uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD).
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