Accurate de novo and transmitted indel detection in exome-capture data using microassembly

作者：Narzisi Giuseppe^*; O'Rawe Jason A; Iossifov Ivan; Fang Han; Lee Yoon ha; Wang Zihua; Wu Yiyang; Lyon Gholson J; Wigler Michael; Schatz Michael C

来源：Nature Methods, 2014, 11(10): 1033-1036.

DOI：10.1038/NMETH.3069

We present an open-source algorithm, Scalpel (http://scalpel.sourceforge.net/), which combines mapping and assembly for sensitive and specific discovery of insertions and deletions (indels) in exome-capture data. A detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for indel discovery, particularly in regions containing near-perfect repeats. We analyzed 593 families from the Simons Simplex Collection and demonstrated Scalpel's power to detect long (>= 30 bp) transmitted events and enrichment for de novo likely gene-disrupting indels in autistic children.

• 出版日期2014-10