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. 2021 Dec 11;37(24):4860-4861.
doi: 10.1093/bioinformatics/btab454.

Unfazed: parent-of-origin detection for large and small de novo variants

Jonathan R Belyeu  1   2 , Thomas A Sasani  1   2   3 , Brent S Pedersen  1   2 , Aaron R Quinlan  1   2
Affiliations

Unfazed: parent-of-origin detection for large and small de novo variants

Jonathan R Belyeu et al. Bioinformatics. .

Abstract

Summary: Unfazed is a command-line tool to determine the parental gamete of origin for de novo mutations from paired-end Illumina DNA sequencing reads. Unfazed uses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants to de novo mutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites. Unfazed provides a simple command-line interface and scales well to large inputs, determining parent-of-origin for nearly 30 000 de novo variants in under 60 h.

Availability and implementation: Unfazed is available at https://github.com/jbelyeu/unfazed.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Unfazed identifies the origin parent for variants by extended read-based phasing. (A) Read-based phasing uses reads overlapping a site of interest and a phase informative site to identify the origin parent. (B) Extended read-based phasing chains reads to include information from non-overlapped phase-informative sites. (C) Extended read-based phasing can be applied to SVs by using discordant pairs or split reads
See this image and copyright information in PMC

References

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