Recurrent miscalling of missense variation from short-read genome sequence data.

ABSTRACT:

Background

Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases of genomic variation.

Results

We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of

SUBMITTER: Field MA 

PROVIDER: S-EPMC6631443 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature