Scalpel statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Indel detection chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

Scalpel specifications


Unique identifier OMICS_05395
Name Scalpel
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl
Computer skills Advanced
Version 0.5.4
Stability Stable
Maintained Yes



Add your version


  • person_outline Giuseppe Narzisi <>

Publications for Scalpel

Scalpel in publications

PMCID: 5906580
PMID: 29670134
DOI: 10.1038/s41598-018-24400-4

[…] by removing all variants identified in sequencing data of three olaparib-sensitive an3-12 clones using vcftools vcf-isec; indels were further verified by using the microassembly-based variant caller scalpel. to address the high false positive rate in indel variant calls, only the indels that were identified by both variant callers and have passed the filters were retained., variants […]

PMCID: 5506390
PMID: 28740869
DOI: 10.1212/NXG.0000000000000164

[…] duplicate reads using picard tools and realignment around indels and base recalibration using genome analysis toolkit (gatk) version 2.7.4. mutect v1.1.4, lofreq v2.0.0, strelka v1.0.13, pindel, and scalpel were used to return the union of variant calls. variants were filtered out if they were at >1% frequency in the 1000 genomes or exac data sets, had more than 2 alleles to remove artifacts, […]

PMCID: 5164930
PMID: 27820796
DOI: 10.1038/nchembio.2226

[…] as well as variants present in sequencing of a mouse strain from the 129s5 background. indels called from whole exome sequencing data were further verified using the microassembly based caller scalpel and discarded from the data if not identified by both callers. all remaining variants were used to generate a visualization of mutational patterns. all snvs were assigned to one of 96 […]

PMCID: 5010666
PMID: 27590916
DOI: 10.1186/s12864-016-3045-z

[…] packages are available for both single- and multi-sample variant calling, such as samtools [], freebayes [], gatk unifiedgenotyper and haplotypecaller [, ]. packages like gatk haplotypecaller, scalpel [] and platypus [] combine mapping and local assembly, which are particularly attractive for indel detection., numerous studies have compared the performance of variant callers on wes, […]

PMCID: 4968449
PMID: 27480531
DOI: 10.1186/s13059-016-1024-y

[…] cnd or lumpy, and a secondary breakpoint, which are the outer bounds of merged deletions., to identify sv insertions, retroseq (transposable element insertions) [], cnd (copy number gains) [], scalpel [] and manta (both novel sequence insertions) [] were used. parameters for each analysis are contained in table s5 of additional file ., calls made by each tool were then filtered to remove […]

To access a full list of publications, you will need to upgrade to our premium service.

Scalpel institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Stony Brook University, Stony Brook, NY, USA; New York Genome Center, New York, NY, USA; Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico; Columbia University Medical Center, New York, NY, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Scalpel funding source(s)
Supported by grants from the US National Institutes of Health (R01-HG006677 and U01- CA168409) and the US National Science Foundation (DBI-1350041) and by grants from the Cold Spring Harbor Laboratory (CSHL) Cancer Center Support (5P30CA045508), the Stanley Institute for Cognitive Genomics and the Simons Foundation (SF51 and SF235988).

Scalpel reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Scalpel