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SNPFile – A software library and file format for large scale association mapping and population genetics studies

Jesper Nielsen12* and Thomas Mailund1

Author Affiliations

1 Bioinformatics Research Center, University of Aarhus, Denmark

2 Department of Computer Science, University of Aarhus, Denmark

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BMC Bioinformatics 2008, 9:526  doi:10.1186/1471-2105-9-526

Published: 8 December 2008



High-throughput genotyping technology has enabled cost effective typing of thousands of individuals in hundred of thousands of markers for use in genome wide studies. This vast improvement in data acquisition technology makes it an informatics challenge to efficiently store and manipulate the data. While spreadsheets and at text files were adequate solutions earlier, the increased data size mandates more efficient solutions.


We describe a new binary file format for SNP data, together with a software library for file manipulation. The file format stores genotype data together with any kind of additional data, using a flexible serialisation mechanism. The format is designed to be IO efficient for the access patterns of most multi-locus analysis methods.


The new file format has been very useful for our own studies where it has significantly reduced the informatics burden in keeping track of various secondary data, and where the memory and IO efficiency has greatly simplified analysis runs. A main limitation with the file format is that it is only supported by the very limited set of analysis tools developed in our own lab. This is somewhat alleviated by a scripting interfaces that makes it easy to write converters to and from the format.