title: chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts.
abstract: Advances in sequencing capacity have led 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 kb genomic regions, eventually enabling the joint analysis of more than 10 000 individuals.
  
  
  
  The software is implemented in C ++, GPL licensed and available at http://github.com/DecodeGenetics/chopBAIContact:birte.kehr@decode.is.
authors.affiliation: deCODE Genetics/Amgen, Reykjavík, Iceland.
authors.forename: Birte
authors.initials: B
authors.lastname: Kehr
authors.affiliation: deCODE Genetics/Amgen, Reykjavík, Iceland Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavík, Iceland.
authors.forename: Páll
authors.initials: P
authors.lastname: Melsted
mesh_terms: D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006801:Humans; D012984:Software