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FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units

Gang Peng, Yu Fan, Wenyi Wang, Paul P. Gardner
2014 PLoS Computational Biology  
Few variant calling programs, however, utilize the pedigree information when the family-based sequencing data are available.  ...  Various algorithms have been developed for variant calling using next-generation sequencing data, and various methods have been applied to reduce the associated false positive and false negative rates.  ...  Jeffrey Morris for providing the GPU computer to test our software and Zeya Wang for helping us prepare the test data.  ... 
doi:10.1371/journal.pcbi.1003880 pmid:25357123 pmcid:PMC4214554 fatcat:n6u522ejxnhnxc5vqte3hgedwu

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

Aquillah M. Kanzi, James Emmanuel San, Benjamin Chimukangara, Eduan Wilkinson, Maryam Fish, Veron Ramsuran, Tulio de Oliveira
2020 Frontiers in Genetics  
In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying  ...  Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.  ...  Consensus Variant Calling System (CoVaCS) is an automated, highly accurate system with a web-based graphical interface for genotyping and variant annotation of NGS data.  ... 
doi:10.3389/fgene.2020.544162 pmid:33193618 pmcid:PMC7649788 fatcat:dkcsrkvggbbkvhg32l2a4ejlky