G.C. contributed to the structural variant analysis and data visualization.
Variant analysis was performed using the GATK (software.broadinstitute.org) software following the RNA-seq best practices.
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Smith, B. N. et al. Exome-wide Rare Variant Analysis Identifies TUBA4A Mutations Associated with Familial ALS.
For example, over 200 computational tools have been developed for variant analysis of next-generation genome sequencing data33.
Pabinger, S. et al. A survey of tools for variant analysis of next-generation genome sequencing data.
Background: Simulating genome sequence data with variant features facilitates the development and benchmarking of structural variant analysis programs.
Wang, Y., Lu, J., Yu, J., Gibbs, R. A. & Yu, F. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
The FASTQ files were de-multiplexed and aligned to the human reference genome for variant analysis (detailed methods provided in Supplementary Information).
Carss, K. J. et al. Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.
Finally, before analyzing the data for association, we explored the impact of population structure on rare variant analysis in these data.
