Pindel statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


Pindel specifications


Unique identifier OMICS_00321
Name Pindel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The reference genome sequence and a file of one-end-mapped read pairs.
Input format BAM, FASTQ
Output data Information about each indel event at the base level.
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.2.5b8
Stability Stable
Maintained Yes




No version available



  • person_outline Zemin Ning
  • person_outline Kai Ye

Publication for Pindel

Pindel citations


Germline mutation in the TP53 gene in uveal melanoma

Sci Rep
PMCID: 5955881
PMID: 29769598
DOI: 10.1038/s41598-018-26040-0

[…] NextGENe® Software was used for the analysis of the sequencing data, and CNV analysis. The Pindel tool was used to detect break points of large deletions and medium sized insertions. The R package SNPRelate was performed to exclude unknown family relationships. […]


A genome wide survey of mutations in the Jurkat cell line

BMC Genomics
PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] kDancer, and CNVnator [–].The Genome Analysis Toolkit (GATK) from the Broad Institute uses De Bruijn graph-based models to identify single-nucleotide substitutions and small insertions and deletions. Pindel’s split-read approach can also detect small insertions and deletions, as well as inversions, tandem duplications, and inter-chromosomal translocations. BreakDancer compares the distance between […]


Compound heterozygous TYK2 mutations underlie primary immunodeficiency with T cell lymphopenia

Sci Rep
PMCID: 5934390
PMID: 29725107
DOI: 10.1038/s41598-018-25260-8
call_split See protocol

[…] ttps://, followed by data annotation using the Illumina VariantStudio software. Analyses of the SVs from the exome sequencing data were performed using the programs, Pindel, Delly and gridss (, at their default settings. For Sanger DNA sequencing, coding regions of the TYK2 gene were amplified from the synthesized cDNA using […]


Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS based analysis of hereditary cancer syndromes

PLoS One
PMCID: 5896995
PMID: 29649263
DOI: 10.1371/journal.pone.0195761

[…] ome in male and female probands () that also demonstrates the dynamic range of analysis in detection of real deletion.For the detection of medium-size insertions and tandem duplications, we added the Pindel tool to the bioinformatics pipeline in order to identify the 64 bp tandem duplication in BRCA1 (c.5468-11_5520dup64; NM_007294; Chr17: 41197765–41197830 on Assembly GRCh37) not detected by GATK […]


Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers

PLoS One
PMCID: 5894988
PMID: 29641532
DOI: 10.1371/journal.pone.0194098

[…] hm was used to map sequence reads to the UCSC human genome reference build 19 []. SNVs were detected using bcftools and SAMtools mpileup with disabled BAQ computation [] and indels were detected with pindel [] and annotated to dbSNP144 by ANNOVAR []. Variants altering the coding sequence were selected that were present at a frequency of <1:100 (0.01) in the Kaviar aggregated control population [] […]


IMSindel: An accurate intermediate size indel detection tool incorporating de novo assembly and gapped global local alignment with split read analysis

Sci Rep
PMCID: 5884821
PMID: 29618752
DOI: 10.1038/s41598-018-23978-z

[…] ls have been developed to detect these intermediate-size indels. They can mainly be classified into three approaches: (1) realignment based approach (GATK, Scalpel, SV-STAT), (2) split-read approach (PINDEL, Splitread, PRISM), and (3) local assembly approach (SOAPindel). Recently, hybrid approaches that integrate these approaches have also been developed, resulting in more sensitive indel discover […]


Looking to check out a full list of citations?

Pindel institution(s)
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Netherlands; Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany; The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Pindel funding source(s)
Supported by NGI/EBI fellowship 050-72-436 from Netherlands Genomics Initiative.

Pindel reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Pindel