Indelocator protocols

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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 in pipelines

 (4)
2017
PMCID: 5529435
PMID: 28747664
DOI: 10.1038/s41598-017-06811-x

[…] all amplification products have the same start and stop positions making it impossible to distinguish different dna fragments from pcr duplicate reads. snvs were identified using mutect, indels with indelocator and annovar to annotate the identified variants. we applied the same additional filters we used for wes analysis to the identified snvs and indels., we checked for a higher frequency […]

2016
PMCID: 4975391
PMID: 27494029
DOI: 10.1371/journal.pgen.1006242

[…] with variant af between 0.05 and 0.95. allele frequencies for these snps for each sample were graphed according to nucleotide position using excel., all sequence variants identified by mutect and indelocator were reviewed. those identified in intronic and intergenic regions, and in ncrna; or with a total number of variant reads < 3 or reads present only in one direction; or those seen […]

2015
PMCID: 4517542
PMID: 26221190
DOI: 10.1186/s13148-015-0091-3

[…] removed (picard). gatk6 was used to refine the alignments near insertion/deletion (indel) sites. single nucleotide variants (snvs) were called using mutect7, and indels were called using indelocator (http://www.broadinstitute.org/cancer/cga/indelocator). annotation was performed using oncotator. because tumor tissues were sequenced without a paired normal from the corresponding […]

2014
PMCID: 4224628
PMID: 24909177
DOI: 10.1038/onc.2014.150

[…] pipeline. briefly, reads were aligned using bwa, followed by indel realignment and quality score recalibration using the genome analysis toolkit. somatic mutations were detected using mutect and indelocator, then annotated using oncotator (http: //www.broadinstitute.org/oncotator). mutsig v.1.5 was used to detect significantly mutated genes. copy-number calls were derived from relative […]


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Indelocator in publications

 (31)
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 […]

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 […]

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 […]

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 […]

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, […]


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