PT - JOURNAL ARTICLE AU - Stephane E. Castel AU - Pejman Mohammadi AU - Wendy K. Chung AU - Yufeng Shen AU - Tuuli Lappalainen TI - Rare Variant Phasing and Haplotypic Expression from RNA-Sequencing with phASER AID - 10.1101/039529 DP - 2016 Jan 01 TA - bioRxiv PG - 039529 4099 - http://biorxiv.org/content/early/2016/06/03/039529.short 4100 - http://biorxiv.org/content/early/2016/06/03/039529.full 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.