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Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms CRISP

Detects SNPs and short indels from high-throughput sequencing of pooled DNA samples. CRISP has been primarily developed to analyze data from "artificial" DNA pools, i.e. pools generated by equi-molar pooling of DNA from multiple individual samples. CRISP leverages sequence data from multiple such pools to detect both rare and common variants. Note that the method is not designed for variant detection from a single pool. CRISP was developed for targeted disease association studies in humans but may work well for other applications.

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CRISP classification

CRISP specifications

Software type:
Restrictions to use:
Output data:
Single file with information about the variants and the genotypes (or allele frequencies) for each pool or sample
Operating system:
Computer skills:
Command line interface
Input format:
Output format:
Programming languages:


  • piCALL

CRISP distribution


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CRISP support


  • Vikas Bansal <>


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Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA, USA

Funding source(s)

Scripps Translational Science Institute Clinical Translational Science Award (National Institutes of Health U54RR02504-01)

Link to literature

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