Tue, Dec 30, 2014 at 3:13 pm
Customer asks about analysis options for human whole-genome sequencing data analysis.
Tue, Dec 30, 2014 at 4:26 PM
AccuraScience LB: AccuraScience LB: Routine processing of a human whole-genome sequencing dataset includes (1) sequencing data quality control, (2) mapping of all reads to the human reference genome, and (3) SNV and indel calling.
Some of the "advanced" analysis tasks you might consider include: (1) Make predictions on the functional consequences (or severity) of identified SNVs/indels using Annovar, and a number of tools including SIFT, PolyPhen2, LTR, and MutationTaster, (2) Pull from "1000-genomes project" data variants from subjects of matching population (assumed to be healthy), and identify SNVs/indels significantly over-represented in your samples as compared to the general population, and (3) Attempt to identify over-represented Gene Ontology terms (or biological pathways) over-represented among the genes carrying the variants identified (especially those predicted to confer severe consequences in (2)).
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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