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ScanIndel specifications


Unique identifier OMICS_16278
Name ScanIndel
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data The listed samples to be analyzed in FastQ file or aligned BAM file, the reference file for each BWA, BLAT and Freebayes.
Output data The VCF file for detected variant and BAM files for BWA-MEM and BLAT mapping
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Bedtools, SAMtools, BWA, BLAT, freebayes, Inchworm assembler, Pysam, PyVCF, Biopython, SciPy, NumPy
Maintained Yes




No version available



  • person_outline Rendong Yang

Publication for ScanIndel

ScanIndel citation


IMSindel: An accurate intermediate size indel detection tool incorporating de novo assembly and gapped global local alignment with split read analysis

Sci Rep
PMCID: 5884821
PMID: 29618752
DOI: 10.1038/s41598-018-23978-z

[…] stein-Barr virus (Human herpesvirus 4)-mediated transformation of peripheral blood mononuclear cells. The samples were used for the accuracy evaluation of our method, GATK HaplotypeCaller, PINDEL and ScanIndel. For real case performance of our method, we also used 478 DNA samples collected from a consortium for congenital neurological diseases and hearing loss after obtaining written informed cons […]

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ScanIndel institution(s)
Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
ScanIndel funding source(s)
This work was supported by funds from the Department of Laboratory Medicine and Pathology at the University of Minnesota and by a Young Investigator Award from the PCF.

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