RT Journal Article
SR Electronic
T1 Rare Variant Phasing and Haplotypic Expression from RNA-Sequencing with phASER
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 039529
DO 10.1101/039529
A1 Stephane E. Castel
A1 Pejman Mohammadi
A1 Wendy K. Chung
A1 Yufeng Shen
A1 Tuuli Lappalainen
YR 2016
UL http://biorxiv.org/content/early/2016/06/03/039529.abstract
AB 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.