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 <>

Pindel article

Pindel citations

PMCID: 4864822

[…] previously identified with sanger sequencing in the ls sample used as a positive control (see table 3 for details). in addition, a class 5 msh6 exon 3 deletion (c.458_627del, ec #20) identified by pindel, was detected in one ec case which we validated using mlpa (see table 3 for details). this frameshift deletion was identified in a patient that was diagnosed with ec at the age of 60 years, […]

PMCID: 4682451

[…] gene was >10x across 91.8% and 82.4% of exonic and intronic dna, respectively. variant calling was performed using gatk [mckenna et al., 2010] and pindel [ye et al., 2009]. variants identified by pindel that had variable allele ratios >0.2 and <0.8 were considered as heterozygous. only variants predicted by reads with phred quality scores >30, which have a 1 in 1,000 chance […]

PMCID: 4394698

[…] was performed on a hiseq2500 system (illumina). bwa (version was used for read alignment to the human reference assembly (hg19). genetic variation was detected using samtools (v 0.1.18), pindel (v 0.2.4t), and exomedepth (v1.0.0). the average coverage was 128-fold and more than 97% of the target region was covered at least 20-fold allowing for high-confidence variant calls. filtering […]

PMCID: 4383019

[…] reads were removed using samtools before analysis. single-nucleotide variant calling was performed using caveman943 and small insertions and deletions were identified using a modified version on pindel in paired tumour-normal mode. the following filtering criteria were applied to the called variants: only nucleotides with phred quality of 20 or greater were considered; only reads mapping […]

PMCID: 4338529

[…] genome (ncbi build grch37/hg19). samtools56 was used to remove pcr duplicates and to call single-nucleotide variants (snv). detection of small insertions and deletions (smindel) was conducted with pindel 0.2.2 software57. the average sequencing coverage was 155× per dna sample (supplementary table 2). the search for somatic mutations was restricted to the regions covered at least 20-fold […]

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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