Variant Calling Pipeline. Article Swipe
YOU?
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· 2015
· Open Access
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· DOI: https://doi.org/10.1371/journal.pone.0133742.g003
· OA: W2240126540
<p>The vcf file created through the project quality control pipeline is filtered for frequency using 1000Genome, dbSNP, ExAC, and NHLBI Exome Project. All variants with a MAF <1% are then prioritized by gene function and genomic region. Variants associated with the patient's phenotype mapping to exons are further prioritized based on functional annotation. If protein-changing variants are identified in a gene of interest, further analysis of non-protein changing variants, UTRs, and intronic regions are analyzed to consider the possibility of compound heterozygous variants. Variants are visualized and reviewed though IGV and <i>In silico</i> prediction tools, and taken into consideration to estimate the possible impact of each variant at the protein level. Variants are also manually investigated through Alamut v2.2 software (Interactive Biosoftware, San Diego, CA) to aid in variant interpretation and pathogenicity predictions. Of note, we follow the ACMG guidelines for incidental findings (grey boxes).</p>
