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Mosdepth: Quick Coverage Calculation for Genomes and Exomes

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2017 Nov 3
PMID 29096012
Citations 443
Authors
Brent S Pedersen
Aaron R Quinlan
Affiliations
Soon will be listed here.
Abstract

Summary: Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM 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 coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced.

Availability And Implementation: mosdepth is available from https://github.com/brentp/mosdepth under the MIT license.

Contact: bpederse@gmail.com.

Supplementary Information: Supplementary data are available at Bioinformatics online.

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