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Protocols

Pindel specifications

Information


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

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Versioning


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Documentation


Maintainers


  • person_outline Zemin Ning
  • person_outline Kai Ye

Publication for Pindel

Pindel citations

 (188)
library_books

Germline mutation in the TP53 gene in uveal melanoma

2018
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. […]

library_books

A genome wide survey of mutations in the Jurkat cell line

2018
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 […]

call_split

Compound heterozygous TYK2 mutations underlie primary immunodeficiency with T cell lymphopenia

2018
Sci Rep
PMCID: 5934390
PMID: 29725107
DOI: 10.1038/s41598-018-25260-8
call_split See protocol

[…] ttps://software.broadinstitute.org/gatk/), 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 (https://github.com/PapenfussLab/gridss), at their default settings. For Sanger DNA sequencing, coding regions of the TYK2 gene were amplified from the synthesized cDNA using […]

library_books

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

2018
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 […]

library_books

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

2018
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 [] […]

library_books

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

2018
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 […]

Citations

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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.

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