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.
Infers the strain numbers and haplotype frequencies in silico from sequences of pooled samples. PoolHap Is an application that was developed to facilitate biological insight into heterogeneous samples that are difficult to isolate experimentally. This method has the possibility to be applied to whole genome sequences of small viruses or individual genes.