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

By Stephane E. Castel, Pejman Mohammadi, Wendy K. Chung, Yufeng Shen, Tuuli Lappalainen

Posted 12 Feb 2016
bioRxiv DOI: 10.1101/039529 (published DOI: 10.1038/ncomms12817)

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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