Pindel protocols

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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



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  • person_outline Zemin Ning <>
  • person_outline Kai Ye <>

Publication for Pindel

Pindel in pipelines

PMCID: 5780457
PMID: 29362368
DOI: 10.1038/s41598-018-19278-1

[…] and if the afs for all the other 23 samples were <5%. the candidate mutation site was defined as homozygous if the af ≥80%, and if the afs for all the other 23 samples were <5%. for the pindel and breakdancer analyses, the candidate mutation sites were sorted by the position in the genome and those unique to a single sample were further considered. all candidate mutations […]

PMCID: 5816515
PMID: 29467591
DOI: 10.1186/s12935-018-0521-3

[…] the raw data. the low-quality variations were filtered out using the quality score ≥ 20 (q20). the sequencing reads were aligned to the ncbi human reference genome (hg19) using bwa. samtools and pindel were used to analyzed snp and indel of the sequence (additional file )., 27 cases of children with stage iv nb, consisted of 15 females and 12 males, with a median age of 39 months (range […]

PMCID: 5824822
PMID: 29476136
DOI: 10.1038/s41467-018-02826-8

[…] sequence (ncbi build 37) using the following software packages: bwa: 0.7.13, samtools: 1.1 (using htslib 1.1), picard tools: 1.97 (1504), gatk: appistry v2015.1.1–3.4.46–0-ga8e1d99, cnvkit: 0.7.2, pindel: 0.2.5b8, satk: appistry v2015.1.1–1-gea45d62, annovar: v2016feb01, freebayes: 0.9.20, and delly: 0.7.2–. single nucleotide variants and insertions/deletions were visualized and verified using […]

PMCID: 5839396
PMID: 29515765
DOI: 10.18632/oncotarget.23882

[…] the resulting bam [] files were preprocessed and base substitutions and small insertions/deletions were called using mutect [] and pindel [], respectively. to overcome the lack of matched normal sample, we generated virtual common normal sequence using in-house pooled normal sequence. this method has been shown to function […]

PMCID: 5843664
PMID: 29520031
DOI: 10.1038/s41467-018-03121-2

[…] gatk best practices of duplicate removal, indel realignment, and recalibration. somatic single-nucleotide variations (snvs) and small insertions and deletions (indels) were detected by mutect and pindel, respectively. in addition, variants were filtered against the exac database using a cut-off of 0.1%. snvs and indels were annotated using snpeff based on ucsc known genes. of the 274 exome […]

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Pindel in publications

PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] tissue by rna sequencing were considered as true variants. to detect single nucleotide variants, we integrated the results of three types of variant caller, which increased the sensitivity. we used pindel to detect indels. all egfr exon 19 deletions were considered as true variants., the library construction for whole transcriptome analyses were performed using the truseq rna sample preparation […]

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

[…] retrieval solution (ph 9.0) overnight at 98 °c for msh2, msh6, mlh1 and for 50 minutes at 98 °c for pms2., 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., used custom ngs panel […]

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

[…] tool uses a certain type of sequence information to identify specific categories of variants. our variant caller suite consisted of four distinct tools and algorithms: the genome analysis toolkit, pindel, breakdancer, 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 […]

PMCID: 5934390
PMID: 29725107
DOI: 10.1038/s41598-018-25260-8

[…] 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 […]

PMCID: 5931590
PMID: 29717121
DOI: 10.1038/s41467-018-04052-8

[…] short reads were aligned to human reference genome grch37/hg19. somatic substitutions, indels and rearrangements in clones and subclones were called by caveman (, pindel, ( and brass (, respectively., de novo somatic mutations of substitutions, indels and rearrangements in subclones […]

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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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