PT  - JOURNAL ARTICLE
AU  - Brent S. Pedersen
AU  - Aaron R. Quinlan
TI  - mosdepth: quick coverage calculation for genomes and exomes
AID  - 10.1101/185843
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 185843
4099  - http://biorxiv.org/content/early/2017/09/07/185843.short
4100  - http://biorxiv.org/content/early/2017/09/07/185843.full
AB  - Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM (Li et al. 2009) or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce optional coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced.Availability mosdepth is available from https://github.com/brentp/mosdepth under the MIT license‥Contact bpederse{at}gmail.com, aaronquinlan{at}gmail.comSupplementary information Detailed documentation is available at https://github.com/brentp/mosdepth