Pindel 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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Maintainers


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

Publication for Pindel

Pindel IN pipelines

 (32)
2018
PMCID: 5839396
PMID: 29515765
DOI: 10.18632/oncotarget.23882

[…] the resulting bam [34] files were preprocessed and base substitutions and small insertions/deletions were called using mutect [35] and pindel [36], 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 […]

2018
PMCID: 5843664
PMID: 29520031
DOI: 10.1038/s41467-018-03121-2

[…] best practices of duplicate removal64, indel realignment, and recalibration. somatic single-nucleotide variations (snvs) and small insertions and deletions (indels) were detected by mutect65 and pindel66, respectively. in addition, variants were filtered against the exac67 database using a cut-off of 0.1%. snvs and indels were annotated using snpeff68 based on ucsc known genes. of the 274 […]

2018
PMCID: 5860705
PMID: 29558483
DOI: 10.1371/journal.pone.0194282

[…] package, and base quality recalibration was performed using the genome analysis toolkit (gatk) program [24]., bioinformatics detection of genomic variation was performed on the eighteen bam files by pindel [25] and softsv softwares [26]. the default parameters were used for both programs. since pindel is not applicable for translocations and translocations inverted, we only chose sv types […]

2018
PMCID: 5860705
PMID: 29558483
DOI: 10.1371/journal.pone.0194282

[…] [24]., bioinformatics detection of genomic variation was performed on the eighteen bam files by pindel [25] and softsv softwares [26]. the default parameters were used for both programs. since pindel is not applicable for translocations and translocations inverted, we only chose sv types of deletions (del), insertions (ins), inversions (inv) and tandem duplications (dup). two standards […]

2018
PMCID: 5860705
PMID: 29558483
DOI: 10.1371/journal.pone.0194282

[…] (ins), inversions (inv) and tandem duplications (dup). two standards were used to filter the raw data. firstly, the short read appeared at least three paired-ends. secondly, two softwares, pindel and softsv, were applying for sv calling and breakpoint prediction. two svs overlapped more than 25 bp were merged into one sv if both of svs were belong to the same variation type […]

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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