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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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