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chevron_left Deletion detection Insertion detection CNV detection Structural variant detection Inversion detection CNV detection CNV detection chevron_right
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SoftSearch specifications


Unique identifier OMICS_00322
Name SoftSearch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A file of aligned reads and the genome to which the reads were aligned.
Input format BAM
Output format VCF
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.4
Stability Stable
Maintained Yes



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  • person_outline Jean-Pierre Kocher <>

Publication for SoftSearch

SoftSearch in publications

PMCID: 5881031
PMID: 29514868
DOI: 10.1098/rsob.170211

[…] construction, illumina sequencing and initial data analysis. snp calling and subtraction of irrelevant snps/short indels were performed as previously described []. large indels were identified by softsearch []. around 12 000 breakpoints were found in strain 4c that was identified as an extragenic suppressor and compared to those found in the pf27 strain [] and in fla11-2 [] to identify indels […]

PMCID: 5517105
PMID: 28776031
DOI: 10.1126/sciadv.1700398

[…] consequences [for example, neurodevelopmental diseases () and autism spectrum disorders ()], we completed in silico sv annotation in the dog and wolf genomes using three programs—svmerge (), softsearch (), and ingap-sv (), which together use all available sv detection algorithms: read pair (rp), short reads (sr), read depth (rd), and assembly-based (as). we annotated 38 deletions, 30 […]

PMCID: 4705683
PMID: 26264669
DOI: 10.1093/nar/gkv828

[…] to different chromosomes or with incorrect orientation) are used to identify a possible breakpoint through clustering the reads as in breakdancer () or pindel (). while prism (), delly () and softsearch () cluster ‘split-reads’ where one of the pair has mapped unambiguously to the reference genome or the cigar value has significant numbers of soft-clipped bases (e.g. partially aligned […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations (rausch et al., ), while softsearch (hart et al., ) is designed for wgs, wes, and cc data. recently, lumpy has been shown to be “especially pronounced when evidence is scarce, either due to low coverage data or low variant […]

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SoftSearch institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Chinahester, MN, USA; Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Chinahester, MN, USA

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