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bioRxiv · 10.1101/030825

chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts

Birte Kehr·Páll Melsted
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Abstract

SummaryAdvances in sequencing capacity have lead to the generation of unprecedented amounts of genomic data. The processing of this data frequently leads to I/O bottlenecks, e. g. when analyzing a small genomic region across a large number of samples. The largest I/O burden is, however, often not imposed by the amount of data needed for the analysis but rather by index files that help retrieving this data. We have developed chopBAI, a program that can chop a BAM index (BAI) file into small pieces. The program outputs a list of BAI files each indexing a specified genomic interval. The output files are much smaller in size but maintain compatibility with existing software tools. We show how preprocessing BAI files with chopBAI can lead to a reduction of I/O by more than 95% during the analysis of 10 Kbp genomic regions, eventually enabling the joint analysis of more than 10,000 individuals.\n\nAvailability and ImplementationThe software is implemented in C++, GPL licensed and available at http://github.com/DecodeGenetics/chopBAI

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Birte Kehr, Páll Melsted. 2015-11-06. chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts. https://doi.org/10.1101/030825

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