title: SOAPindel: efficient identification of indels from short paired reads.
abstract: 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.
authors.affiliation: BGI Shenzhen, Shenzhen 518000, China.
authors.forename: Shengting
authors.initials: S
authors.lastname: Li
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Jianliang
authors.initials: J
authors.lastname: Lu
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Lars
authors.initials: L
authors.lastname: Bolund
authors.forename: Mikkel H
authors.initials: MH
authors.lastname: Schierup
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D005189:False Positive Reactions; D015894:Genome, Human; D060005:Genotyping Techniques / Q000379:methods; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D054643:INDEL Mutation; D020161:Physical Chromosome Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software