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CRISP specifications


Unique identifier OMICS_00057
Alternative name Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms
Software type Package/Module
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
Maintained Yes


  • piCALL


No version available


  • person_outline Vikas Bansal <>

Publications for Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms

CRISP citations


A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] for low-frequency somatic variants, as stated in the gatk documentation and shown by independent studies , . we will also exclude variant callers that are primarily used for pooled-samples such as crisp and thunder , ., the article will be structured as follows. we will first describe the general workflow of somatic snv calling in . next, we will explain the core algorithms of individual […]


Spectrum of mutations in monogenic diabetes genes identified from high throughput DNA sequencing of 6888 individuals

PMCID: 5717832
PMID: 29207974
DOI: 10.1186/s12916-017-0977-3

[…] (v3.0) to generate a bam file. the bam file was sorted and pcr duplicates were removed using the picard [] markduplicates command. subsequently, the bam files for the pools were processed using the crisp variant calling program [] to identify variants (details in additional file : supplementary methods). variants were identified for pooled sequence data for each stage separately but jointly […]


Genome wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

PMCID: 5546710
PMID: 28746337
DOI: 10.1371/journal.pntd.0005816

[…] the raw data were mapped, resulting in an average mapped coverage of 24.47 ± 9.07 per pool. three ‘pooled-sequencing’ aware variant calling approaches were used to analyse the pooled mapping data: crisp [], freebayes (using the pooled-continuous parameter) ( and popoolation2 [](). to ensure that comparisons could be made between all sequencing pools, the raw […]


Variational inference for rare variant detection in deep, heterogeneous next generation sequencing data

PMCID: 5244592
PMID: 28103803
DOI: 10.1186/s12859-016-1451-5

[…] samples []. however, the error rate of normal sequencing samples could be unmatched with the error rate of the target samples, which may cause a problem of making false negatives calls []. crisp compares aligned reads across multiple pools to obtain sequencing errors, and then distinguishes true rare variants from the sequencing errors []. however, the bottleneck of crisp is its low […]


A statistical method for the detection of variants from next generation resequencing of DNA pools

PMCID: 5048073
PMID: 27578802
DOI: 10.1093/bioinformatics/btw520

[…] for a statistical method for the detection of variants from next-generation resequencing of dna pools implementation of this method is available at:, for a probabilistic method for the detection and genotyping of small indels from population-scale sequence data a program implementing this method is available at: […]


Predictive Factors for BRCA1 and BRCA2 Genetic Testing in an Asian Clinic Based Population

PMCID: 4519264
PMID: 26221963
DOI: 10.1371/journal.pone.0134408

[…] for samples sequenced by ngs, reads were aligned to the ucsc human reference genome (hg 19) using the bwa aligner (version 0.5.6). variant calling was done using the gatk unified genotyper [], and crisp pipelines [] (for hiseq)., all mutations identified from sanger sequencing or ngs were annotated using the annovar tool, which provides tools such as sift, polyphen- ii hdiv, polyphen—ii hvar, […]

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CRISP institution(s)
Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA, USA
CRISP funding source(s)
Scripps Translational Science Institute Clinical Translational Science Award (National Institutes of Health U54RR02504-01)

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