ALCHEMY

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes

Features

Populaton genetic model based SNP genotype calling
Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes
Bayesian model provides posterior probabilities of genotype correctness as quality measures
Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs
Multithreaded program for parallel execution on multi-CPU/core systems
Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes

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