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Two SNPs were excluded because their genotypes were automatically defined by the call algorithm in ≤ 90% of the adequate samples.
We then presented them with a mock-up version of the IVRS questionnaire, using audio files to simulate an automated call based on the script of the call algorithm.
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As mentioned above, this can be accomplished by increasing the stringency settings of the calling algorithm [18].
One technical obstacle to GWAS on rare variants is the calling algorithm of microarray based genotyping.
We defined genotype-call error as the proportion of genotypes that were assigned an incorrect genotype by the calling algorithm.
In this situation it is likely that the calling algorithm will select many of these as normals.
Incorporating a knowledge of the sequencing platform's error profile after initial SNV calling, rather than including it as part of the calling algorithm, allows the basic calling algorithms to remain relevant for various iterations of the sequencing technology.
The calling algorithm then uses the GenTrain model and signal intensities to assign ("call") a genotype for each locus and tree.
First, increased information included in the calling algorithm leads to an increased fidelity of calling, with multi-sample calling outperforming single sample calling, and LD-aware methods outperforming both.
This could affect the performance of the calling algorithms.
However, one can think of combining the phasing and the calling algorithms into one probabilistic framework.
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CEO of Professional Science Editing for Scientists @ prosciediting.com