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Statistical Tests for the Detection of Single Nucleotide Polymorphisms (SNPs): A Simulation Approach with Pooled and Un-pooled DNA

Ali Sheikhi, David Ramsey

Abstract



The detection of single nucleotide polymorphisms (SNPs) (sites along the genome at which a population shows variation) is an important topic in statistical genetics, specially when dealing with low frequency variants. Several statistical tests have been developed to detect SNPs using pooled and un-pooled DNA. Pooling individuals increases the probability that a rare variant appears in the sample, however, as the pool size increases the mean number of reads from an individual decreases, making it harder to distinguish reads of a rare variant from errors. In this paper we present a comparison of two statistical tests based on the results of simulations with pooled and un-pooled DNA.

Keywords


Single Nucleotide Polymorphisms (SNPs), DNA, Pooled, Simulation.

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