CRISP statistics

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Citations per year

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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


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  • person_outline Vikas Bansal <>

Publications for Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms

CRISP in pipelines

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

[…] relaxed variant calling parameters of popoolation2 (; 34.4% of snps called by popoolation2 were unique to this tool under the conditions used compared to 2.6% and 6.2% of unique snps called by crisp and freebayes, respectively) and in part due to the stochastic variation in allele detection in low sequence coverage pool-seq data., pool-seq has been used to estimate population genetic […]

PMCID: 3852189
PMID: 23999524
DOI: 10.1038/mp.2013.91

[…] was sequenced to ∼895x per pool, or 45x per individual. reads from the pools were aligned to the human reference genome with the program bwa and variant calling was performed with the program crisp. after quality control, 4798 variants remained for further analysis., all variants passing quality-control filters were annotated using a suite of computational and bioinformatics techniques […]

PMCID: 3531709
PMID: 23293637
DOI: 10.3389/fimmu.2012.00386

[…] for ig genes because they are longer than illumina reads and they cannot be aligned to a specific region in the genome due to the enormous variability and randomness of ig gene rearrangements. picall (bansal and libiger, ) also detects indels using a probabilistic method, but it works on a population of diploid individuals. therefore, picall is not suitable for ig gene sequences, […]

PMCID: 3150297
PMID: 21756356
DOI: 10.1186/1471-2105-12-287

[…] approaches, so we could not compare them directly to camba. moreover, these other approaches identify mutations but not the individuals in the populations that carry them. we modified varscan and crisp, the best performing ones from a previous study [], in order to compare them to camba and report those studies in the results section., overlapping pool designs for high-throughput resequencing […]

PMCID: 3238183
PMID: 21884576
DOI: 10.1186/gm273

[…] proportion of read pairs aligning to the same location to be biological rather than pcr duplicates. hence, duplicate removal was not performed., variant calling was performed using version 3 of crisp [], a variant detection algorithm designed specifically for pooled dna samples. default settings were used (minimum read mapping/base quality to consider a read/base for variant calling 10; ≥ 1 […]

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CRISP in publications

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 […]

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 […]

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 […]

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 […]

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: […]

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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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