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Detects redundant indels. Vindel, a simple yet effective computational pipeline, can be used to check whether a set of indels are redundant with respect to those already in the database of interest such as NCBI inverted question marks dbSNP. Of the approximately 5.9 million indels we examined, nearly 0.6 million are redundant, revealing a serious limitation in the current indel annotation. Statistics results prove the consistency of the pipeline on indel redundancy detection for all 22 chromosomes. Apart from the standalone Vindel pipeline, the indel redundancy check algorithm is also implemented in the web server.

Software type:
Pipeline
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
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Software type:
Pipeline
Interface:
Web user interface
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Basic
Stability:
Stable
View all reviews

0 user review

No review has been posted.

View all issues

0 issue

No open issue.

Maintainer

  • Liqing Zhang <lqzhang at vt.edu>

Institution(s)

Department of Computer Science, Virginia Tech, Blacksburg 24061, VA, USA; Department of Statistics, Virginia Tech, Blacksburg 24061, VA, USA

  • (Li et al., 2014) Vindel: a simple pipeline for checking indel redundancy. BMC bioinformatics.
    PMID: 25407965
  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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