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

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. Few variant calling programs, however, utilize the pedigree information when the family-based sequ...

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Main Authors:	Peng, Gang, Fan, Yu, Wang, Wenyi
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214554/

id	pubmed-4214554
recordtype	oai_dc
spelling	pubmed-42145542014-11-05 FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units Peng, Gang Fan, Yu Wang, Wenyi Research Article 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. Few variant calling programs, however, utilize the pedigree information when the family-based sequencing data are available. Here, we present a program, FamSeq, which reduces both false positive and false negative rates by incorporating the pedigree information from the Mendelian genetic model into variant calling. To accommodate variations in data complexity, FamSeq consists of four distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, a graphics processing unit version of the Bayesian network algorithm, the Elston-Stewart algorithm and the Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA graphics processing unit. In order to compare the difference in the four methods, we applied FamSeq to pedigree sequencing data with family sizes that varied from 7 to 12. When there is no inbreeding loop in the pedigree, the Elston-Stewart algorithm gives analytical results in a short time. If there are inbreeding loops in the pedigree, we recommend the Bayesian network method, which provides exact answers. To improve the computing speed of the Bayesian network method, we parallelized the computation on a graphics processing unit. This allowed the Bayesian network method to process the whole genome sequencing data of a family of 12 individuals within two days, which was a 10-fold time reduction compared to the time required for this computation on a central processing unit. Public Library of Science 2014-10-30 /pmc/articles/PMC4214554/ /pubmed/25357123 http://dx.doi.org/10.1371/journal.pcbi.1003880 Text en © 2014 Peng et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Peng, Gang Fan, Yu Wang, Wenyi
spellingShingle	Peng, Gang Fan, Yu Wang, Wenyi FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
author_facet	Peng, Gang Fan, Yu Wang, Wenyi
author_sort	Peng, Gang
title	FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
title_short	FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
title_full	FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
title_fullStr	FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
title_full_unstemmed	FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
title_sort	famseq: a variant calling program for family-based sequencing data using graphics processing units
description	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. Few variant calling programs, however, utilize the pedigree information when the family-based sequencing data are available. Here, we present a program, FamSeq, which reduces both false positive and false negative rates by incorporating the pedigree information from the Mendelian genetic model into variant calling. To accommodate variations in data complexity, FamSeq consists of four distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, a graphics processing unit version of the Bayesian network algorithm, the Elston-Stewart algorithm and the Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA graphics processing unit. In order to compare the difference in the four methods, we applied FamSeq to pedigree sequencing data with family sizes that varied from 7 to 12. When there is no inbreeding loop in the pedigree, the Elston-Stewart algorithm gives analytical results in a short time. If there are inbreeding loops in the pedigree, we recommend the Bayesian network method, which provides exact answers. To improve the computing speed of the Bayesian network method, we parallelized the computation on a graphics processing unit. This allowed the Bayesian network method to process the whole genome sequencing data of a family of 12 individuals within two days, which was a 10-fold time reduction compared to the time required for this computation on a central processing unit.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214554/
_version_	1613150494739398656

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

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