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Publication for SPLITREAD
IMSindel: An accurate intermediate size indel detection tool incorporating de novo assembly and gapped global local alignment with split read analysis
[…] been developed to detect these intermediate-size indels. They can mainly be classified into three approaches: (1) realignment based approach (GATK, Scalpel, SV-STAT), (2) split-read approach (PINDEL, Splitread, PRISM), and (3) local assembly approach (SOAPindel). Recently, hybrid approaches that integrate these approaches have also been developed, resulting in more sensitive indel discovery method […]
A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data
[…] to 1 Mbp building on the split-read approach of Pindel . The algorithms used by SAMtools and GATK limit the size of structural variants, with variants greater than 15 bp rarely being identified . Splitread anchors one end of a read and clusters the unanchored ends to identify size, content, and location of structural variants . When compared to GATK, Splitread called 70% of the same INDELs b […]
Detection of Genomic Structural Variants from Next Generation Sequencing Data
[…] SSAHA2 [Sequence Search and Alignment by Hashing Algorithm, Ning et al. ()], BWA, or Mosaik. It must be stressed that the latest version of Pindel integrates RP to the SR information (Lin et al., ). Splitread searches for clusters of split reads using balanced splits as seeds. Splitread can detect, at least in theory, deletions without size limitation, while for insertions the size spectrum depen […]
The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes
[…] than ten deletions in those random regions in both Neandertal and Denisovan genomes, indicating that a false discovery rate is essentially lower than 5% for both genomes.We used a modified version of SPLITREAD approach (http://splitread.sourceforge.net/, last accessed December 10, 2014) to remap the Neandertal and Denisovan reads to the junctions of the breakpoints of deletions as defined in 1KG d […]
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