h5vc: scalable nucleotide tallies with HDF5.
CONCLUSIONS
As applications of genome sequencing, including exomes and whole genomes, are expanding, there is a need for analysis tools that are scalable to large sets of samples and/or ultra-deep coverage. Many current tool chains are based on the widely used file formats BAM and VCF or VCF-derivatives. However, for some desirable analyses, data management with these formats creates substantial implementation overhead, and much time is spent parsing files and collating data. We observe that a tally data structure, i.e. the table of counts of nucleotides × samples × strands × genomic positions, provides a reasonable intermediate level of abstraction for many genomics analyses, including single nucleotide variant (SNV) and InDel calling, copy-number estimation and mutation spectrum analysis. Here we present h5vc, a data structure and associated software for managing tallies. The software contains functionality for creating tallies from BAM files, flexible and scalable data visualization, data quality assessment, computing statistics relevant to variant calling and other applications. Through the simplicity of its API, we envision making low-level analysis of large sets of genome sequencing data accessible to a wider range of researchers.


METHODS
The package H5VC for the statistical environment R is available through the Bioconductor project. The HDF5 system is used as the core of our implementation.


BACKGROUND
pyl@embl.de or whuber@embl.de


BACKGROUND
Supplementary data are available at Bioinformatics online.
EMBL Heidelberg, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
Paul Theodor
PT
Pyl
Julian
J
Gehring
Bernd
B
Fischer
Wolfgang
W
Huber
D002874:Chromosome Mapping; D059472:Exome; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009711:Nucleotides / Q000032:analysis*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D009711:Nucleotides