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bioRxiv · 10.1101/039529

Rare variant phasing and haplotypic expression from RNA-sequencing with phASER

Stephane E Castel·Pejman Mohammadi·Wendy K Chung·Yufeng Shen·Tuuli Lappalainen
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Abstract

Haplotype phasing of genetic variants is important for clinical interpretation of the genome, population genetic analysis, and functional genomic analysis of allelic activity. Here we present phASER, a fast and accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA-sequencing (RNA-seq), which often span multiple exons due to splicing. This provides 1) dramatically more accurate phasing of rare and de novo variants compared to population-based phasing; 2) phasing of variants in the same gene up to hundreds of kilobases away which cannot be obtained from DNA-sequencing reads; 3) high confidence measures of haplotypic expression, greatly improving power for allelic expression studies.

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Stephane E Castel, Pejman Mohammadi, Wendy K Chung, Yufeng Shen, Tuuli Lappalainen. 2016-02-12. Rare variant phasing and haplotypic expression from RNA-sequencing with phASER. https://doi.org/10.1101/039529

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