indelMINER specifications

Information


Unique identifier OMICS_07704
Name indelMINER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data IndelMINER relies on a combination of split-read and paired-end read approaches to identify indels from a BAM file for a sample.
Input format BAM
Output format The output is provided in the VCF format along with additional information about the variant, including information about its presence or absence in another sample.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Aakrosh Ratan

Publication for indelMINER

indelMINER citations

 (2)
library_books

The association of insertions/deletions (INDELs) and variable number tandem repeats (VNTRs) with obesity and its related traits and complications

2017
PMCID: 5471687
PMID: 28615046
DOI: 10.1186/s40101-017-0142-x

[…] sity and related traits. With the advent of faster and cheaper next-generation genome and exome sequencing, paired with the rise of the software availability for genome-wide detection of INDELs (like indelMINER []) and VNTRs (like VNTRseek []), it is hoped that association and functional characterization studies between INDELs/VNTRs and obesity should be continued and not neglected. […]

library_books

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

2016
Int J Genomics
PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] NER is a compilation of tools that takes the strengths of split-read and de novo assembly to determine INDELs from paired-end reads of WGS data []. Comparisons were done between SAMtools, Pindel, and indelMINER on a simulated dataset with 7,500 INDELs []. SAMtools found the least INDELs with 6,491, followed by Pindel with 7,239 and indelMINER with 7,365 INDELs identified. However, indelMINER's fal […]

indelMINER institution(s)
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, Wartik Laboratory, University Park, PA, USA

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