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- Title
chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts.
- Authors
Kehr, Birte; Melsted, Páll
- Abstract
Summary: 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.
- Subjects
GENOMICS; GENE expression; MOLECULAR genetics; COMPUTER algorithms; GENETIC regulation
- Publication
Bioinformatics, 2016, Vol 32, Issue 14, p2202
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btw149