TY  - JOUR
A1  - Li, Shengting
A1  - Li, Ruiqiang
A1  - Li, Heng
A1  - Lu, Jianliang
A1  - Li, Yingrui
A1  - Bolund, Lars
A1  - Schierup, Mikkel H.
A1  - Wang, Jun
T1  - SOAPindel: Efficient identification of indels from short paired reads
Y1  - 2013/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 195 
EP  - 200 
DO  - 10.1101/gr.132480.111 
VL  - 23 
IS  - 1 
UR  - http://genome.cshlp.org/content/23/1/195.abstract 
N2  - We present a new approach to indel calling that explicitly exploits that indel differences between a reference and a sequenced sample make the mapping of reads less efficient. We assign all unmapped reads with a mapped partner to their expected genomic positions and then perform extensive de novo assembly on the regions with many unmapped reads to resolve homozygous, heterozygous, and complex indels by exhaustive traversal of the de Bruijn graph. The method is implemented in the software SOAPindel and provides a list of candidate indels with quality scores. We compare SOAPindel to Dindel, Pindel, and GATK on simulated data and find similar or better performance for short indels (<10 bp) and higher sensitivity and specificity for long indels. A validation experiment suggests that SOAPindel has a false-positive rate of ∼10% for long indels (>5 bp), while still providing many more candidate indels than other approaches. 
ER  -