RT Journal Article
SR Electronic
T1 SeqHBase: a big data toolset for family based sequencing data analysis
JF Journal of Medical Genetics
JO J Med Genet
FD BMJ Publishing Group Ltd
SP 282
OP 288
DO 10.1136/jmedgenet-2014-102907
VO 52
IS 4
A1 Min He
A1 Thomas N Person
A1 Scott J Hebbring
A1 Ethan Heinzen
A1 Zhan Ye
A1 Steven J Schrodi
A1 Elizabeth W McPherson
A1 Simon M Lin
A1 Peggy L Peissig
A1 Murray H Brilliant
A1 Jason O'Rawe
A1 Reid J Robison
A1 Gholson J Lyon
A1 Kai Wang
YR 2015
UL http://jmg.bmj.com/content/52/4/282.abstract
AB Background Whole-genome sequencing (WGS) and whole-exome sequencing (WES) technologies are increasingly used to identify disease-contributing mutations in human genomic studies. It can be a significant challenge to process such data, especially when a large family or cohort is sequenced. Our objective was to develop a big data toolset to efficiently manipulate genome-wide variants, functional annotations and coverage, together with conducting family based sequencing data analysis. Methods Hadoop is a framework for reliable, scalable, distributed processing of large data sets using MapReduce programming models. Based on Hadoop and HBase, we developed SeqHBase, a big data-based toolset for analysing family based sequencing data to detect de novo, inherited homozygous, or compound heterozygous mutations that may contribute to disease manifestations. SeqHBase takes as input BAM files (for coverage at every site), variant call format (VCF) files (for variant calls) and functional annotations (for variant prioritisation). Results We applied SeqHBase to a 5-member nuclear family and a 10-member 3-generation family with WGS data, as well as a 4-member nuclear family with WES data. Analysis times were almost linearly scalable with number of data nodes. With 20 data nodes, SeqHBase took about 5 secs to analyse WES familial data and approximately 1 min to analyse WGS familial data. Conclusions These results demonstrate SeqHBase's high efficiency and scalability, which is necessary as WGS and WES are rapidly becoming standard methods to study the genetics of familial disorders.