PRISM pipeline

PRISM specifications


Unique identifier OMICS_02288
Alternative name Pair Read Informed Split Mapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for Pair Read Informed Split Mapper

PRISM IN pipelines

PMCID: 5734874
PMID: 29252184
DOI: 10.7554/eLife.27469.027

[…] were determined using genome analysis toolkit (gatk) (mckenna et al., 2010; depristo et al., 2011; van der auwera et al., 2013), and we combined the output of several tools including soapindel, prism and pindel (li et al., 2013; jiang et al., 2012; ye et al., 2009) to increase the sensitivity of indels detection. we performed a stringent calling procedure for both snvs and indels […]

PMCID: 3997489
PMID: 24705254
DOI: 10.1038/ng.2936

[…] to map all reads to grch37/hg19 using default parameters25. pcr duplicates were removed from alignments using picardtools 1.77 (supplementary table 6). structural variants (sv) were identified using prism 1.1.6 and prism ctx 1.0.126. recurrent svs (supplementary table 7) were found after subtracting common svs27 and all svs found in normal tissue and were visually validated using dnac algorithm […]

PRISM institution(s)
Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China

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