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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

Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] ly 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 variant […]


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

[…] g (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 acro […]


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

PLoS Negl Trop Dis
PMCID: 5546710
PMID: 28746337
DOI: 10.1371/journal.pntd.0005816

[…] of 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 seq […]


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

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

[…] We compared the performance of our variational EM algorithm with the state-of-the-art variant detection methods, SAMtools [], GATK [], CRISP [], VarScan2 [], Strelka [], SNVer [], MuTect [], and RVD2 [], using synthetic DNA data set (Table ). Among all of the methods compared, our variational EM algorithm has a higher sensitivity and […]


Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering

Sci Rep
PMCID: 5037392
PMID: 27670852
DOI: 10.1038/srep33735

[…] We have used CRISP (v27122013) as the variant caller. CRISP takes as input the BAM files (HQ-BAMs in our case) of individual pools and the reference human genome in standard FASTA format. To call the variants only […]


Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies

PMCID: 4938651
PMID: 27172202
DOI: 10.1534/g3.116.028753

[…] ition to be around 200. At positions with a depth lower than 200, all reads were retained. Finally, SNP identification and allele frequency estimation were performed in all sequencing libraries using CRISP, a multi-sample variant caller for high-throughput pooled sequence data (). To minimize the number of possible sequencing errors, the inference of an allele and its frequency was considered to b […]


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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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