Rxivist logo

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.

Download data

  • Downloaded 1,675 times
  • Download rankings, all-time:
    • Site-wide: 7,479 out of 116,126
    • In genetics: 407 out of 5,126
  • Year to date:
    • Site-wide: 50,170 out of 116,126
  • Since beginning of last month:
    • Site-wide: 26,281 out of 116,126

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)