NGS data preprocessing. Handling sequence files. Quality control tools.NGS data preprocessing
Mapping. Reference genome as a concept. NGS alignment programs and algorithms. SAM/BAM and BED file formats overview. Mapped reads visualization. Quality control of the mapping. Local realignment. Computational needs.MappingVisualization
Variant Calling. Variant types: SNPs and InDels. Calling procedures and algorithms. VCF file formats overview. Introduction to the programs GATK, Annovar and Variant. Variant filtering. The problem of the missing data. Variant annotation. Data bases and data repositories: dbSNP, the 1000 Genomes Project and CIBERER Spanish Variant Server.Variant Calling
13:30 – 15:00 Lunch break
Will be held in the cafeteria of the CIPF.
15:00 – 17:30 Prioritization of variants and genes
BiERapp. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies. (Presentation).
CSVS (CIBERER Spanish Variant Server). This database provides information about the variability of the Spanish population. It is very useful for filtering polymorphisms and local variations when prioritizing candidate disease genes. CSVS
Babelomics 5.0: functional interpretation for new generations of genomic data. Alonso R, Salavert F, Garcia-Garcia F, et al. Nucleic Acids Res. 2015;43:W117-W121.
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J. Nucleic Acids Res. 2015;43:W270-W275.
Understanding disease mechanisms with models of signaling pathway activities. Sebastian-Leon P, Vidal E, Minguez P, et al. BMC Syst Biol. 2014;8(1):121.
Inferring the functional effect of gene expression changes in signaling pathways. Sebastián-León P, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J. Nucleic Acids Res. 2013;41:W213-W217.
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W88-W93.
A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Alemán A, Garcia-Garcia F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W83-W87.
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. Nucl. Acids Res. 2009;37:W109-114