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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.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Input format:
BAM
Output data:
Single file with information about the variants and the genotypes (or allele frequencies) for each pool or sample
Output format:
VCF
Operating system:
Unix/Linux
Programming languages:
C
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Vikas Bansal <vbansal at scripps.edu>

Institution(s)

Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA 92037, USA

Funding source(s)

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

  • (Bansal, 2010) A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics.
    PMID: 20529923

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