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A Bayesian method to call indels from short-read sequence data in individuals and populations by realigning reads to candidate haplotypes that represent alternative sequence to the reference. The candidate haplotypes are formed by combining candidate indels and SNVs identified by the read mapper, while allowing for known sequence variants or candidates from other methods to be included. In our probabilistic realignment model we account for base-calling errors, mapping errors, and also, importantly, for increased sequencing error indel rates in long homopolymer runs.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Input data:
Mapped Illumina read data
Input format:
BAM
Output data:
Variant calls
Output format:
VCF
Biological technology:
Illumina
Operating system:
Unix/Linux, Mac OS
Programming languages:
C++
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Cornelis Albers <caa at sanger.ac.uk>

Institution(s)

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, United Kingdom

  • (Albers et al., 2011) Dindel: accurate indel calls from short-read data. Genome research.
    PMID: 20980555

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