Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples.

"data availability the datasets generated for this study were deposited in the european nucleotide archive (ena; project no prjeb48078) and the annotated consensus genome sequences were deposited in ena (accession nos erz4195000 erz4195185 and erz4195400). since hts can lead to errors associated with read directionality ( ) only snvs confirmed by at least two reads in each direction were included thus requiring a coverage depth of >=4 reads/nt 2 6 for each snv reads calling the alternative nucleotide were identified using sam2tsv ( http://dx doi org/10 6084/m9 figshare 1425030 ). data availability the datasets generated for this study were deposited in the european nucleotide archive (ena; project no prjeb48078"

"a conda environment with all the tools and resources used in the pipeline is available ( https://github com/josephhughes/hcmvmut )."

"Conflict of interest: None declared."

"Funding This project was supported by the Medical Research Council (grant number MC_UU_12014/3) and the Wellcome Trust (grant number 204870/Z/16/Z). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author-accepted manuscript version arising from this submission."