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Indelocator specifications

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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

 (31)
library_books

Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair

2018
Nat Commun
PMCID: 5931517
PMID: 29717118
DOI: 10.1038/s41467-018-04002-4

[…] (bam files) of the 547 tcga exomes were downloaded from the genome data commons (gdc). somatic point mutations were called using mutect and filtered using d-toxog, and indels were called using indelocator (all available at http://www.broadinstitute.org/cancer/cga). all calls were filtered using a panel of normals. indels in microsatellite loci were called using msmutect., to identify […]

library_books

Rituximab Treatment Prevents Lymphoma Onset in Gastric Cancer Patient Derived Xenografts12

2018
PMCID: 5915970
PMID: 29574251
DOI: 10.1016/j.neo.2018.02.003

[…] hybrid capture with a focused targeted bait set of 243 genes selected based upon their alteration in prior studies of gastroesophageal cancer. somatic events were identified with mutect v1.1.4 and indelocator (http://www.broadinstitute.org/cancer/cga/indelocator). additionally, sequencing was performed on a germline dna sample from nod-scid mice and putative somatic alterations detected […]

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

[…] 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 […]

library_books

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

[…] 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 […]

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

[…] matched normal samples ()., 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, […]

library_books

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

[…] 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 […]


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