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Protocols

Indelocator specifications

Information


Unique identifier OMICS_00098
Name Indelocator
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM
Output data A high-sensitivity list of putative indel events containing large numbers of false positives.
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability No
Maintained No

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Indelocator citations

 (29)
library_books

Xome Blender: A novel cancer genome simulator

2018
PLoS One
PMCID: 5886411
PMID: 29621252
DOI: 10.1371/journal.pone.0194472

[…] rst analyzes separately the aligned reads in tumor and normal samples and than post-process the resulting variants by applying an additional set of filters [].To call insertions and deletions we used Indelocator that isn’t part of the current MuTect distribution. In its default mode, Indelocator uses the same inputs of MuTect. Without performing realignment or split-read alignment, the tool looks […]

call_split

Dissecting the Mutational Landscape of Cutaneous Melanoma: An Omic Analysis Based on Patients from Greece

2018
PMCID: 5923351
PMID: 29596374
DOI: 10.3390/cancers10040096
call_split See protocol

[…] s previously presented []. For this study, we used version 3.6 of GATK [], which incorporates somatic SNP calling with somatic indel (insertions & deletions) calling, as carried out by MuTect2 [] and Indelocator [], comparing the tumour-normal pairs in order to characterise somatic mutations. Strand-specific artefacts, possibly due to DNA damage resulting from formalin fixation and storage time, w […]

library_books

Genomics of a pediatric ovarian fibrosarcoma. Association with the DICER1 syndrome

2018
Sci Rep
PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] rformed using an Illumina HiSeq 2000 with the V3 Sequencing kits and the Illumina 1.3.4 pipeline (Illumina, CA). For variant calling, we used MuTect ver 1.1.4 in High Confidence mode (HC) for SNV and InDelocator for small insertions and deletions. Variants were annotated with Oncotator. Non-coding variants, with the exception of splice-site mutations were excluded. SNVs and InDels were further fil […]

call_split

Imaging genotyping of functional signaling pathways in lung squamous cell carcinoma using a radiomics approach

2018
Sci Rep
PMCID: 5818618
PMID: 29459639
DOI: 10.1038/s41598-018-21706-1
call_split See protocol

[…] ools.sourceforge.net/SAM1.pdf). BAM files for matched tumor and normal samples were further processed and analyzed in the cancer genome analysis pipeline Firehose. Components include ContEst, Mutect, Indelocator, and dRanger,–. Significance of mutations was calculated using the MutSig algorithm,, and implemented as described previously. The outline of the entire pipeline can be accessed at www.bro […]

library_books

Identification of metastasis driver genes by massive parallel sequencing of successive steps of breast cancer progression

2018
PLoS One
PMCID: 5749725
PMID: 29293529
DOI: 10.1371/journal.pone.0189887

[…] On the exome sequencing data, somatic variant calling was performed using nine publicly available somatic variant callers: EB Call [], Mutect [], Seurat [], Shimmer [], Indelocator (http://www.broadinstitute.org/cancer/cga/indelocator), Somatic Sniper [], Strelka [], Varscan 2 [] and Virmid []. The union of putative somatic mutations, except positions in intronic, in […]

call_split

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy

2017
Nat Commun
PMCID: 5736707
PMID: 29259203
DOI: 10.1038/s41467-017-02329-y
call_split See protocol

[…] hich was in turn used to estimate the lowest allelic fraction at which somatic mutations could be detected on a per-sample basis. Candidate indels (small insertions and deletions) were detected using Indelocator (http://archive.broadinstitute.org/cancer/cga/indelocator). All mutations were filtered using a panel of normals filter, which removes mutations commonly seen across a large number of sequ […]


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