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SomaticIndelDetector specifications


Unique identifier OMICS_00091
Name SomaticIndelDetector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No


No version available

SomaticIndelDetector citations


The molecular landscape of synchronous colorectal cancer reveals genetic heterogeneity

PMCID: 5932564
PMID: 29546405
DOI: 10.1093/carcin/bgy040

[…] gap-aligned reads, mutations should not be significantly enriched within 5 bp of 5′ or 3′ ends of the reads and mutations should not be in simple repeat region. Somatic indels were predicted by GATK SomaticIndelDetector with default parameters. Then, we used our own pipeline to obtain high-confidence somatic indels, as following: combined normal and tumour bam were reused to perform local realign […]


Mutational signatures and chromosome alteration profiles of squamous cell carcinomas of the vulva

PMCID: 5903820
PMID: 29422544
DOI: 10.1038/emm.2017.265

[…] sing and management of marking duplicates, including local realignments and score recalibration. Somatic mutations were detected by comparing tumor and matched normal sequencing data using MuTect and SomaticIndelDetector for point mutations and indels, respectively. ANNOVAR (Annotate Variation) was used for the functional annotation of each variant in the coding regions. PolyPhen-2 was used to pre […]


The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells

PMCID: 5871330
PMID: 29580384
DOI: 10.7554/eLife.31347.034

[…] me and remerged with Picard tools. Summary statistics were computed with GATK (). Somatic point mutations were identified with MuTect (v1.1.4) (). InDels (strand.bias = TRUE) were identified with the SomaticIndelDetector of GATK. Variants were characterized with SnpEff (v3.2a) (). For coverage plots, reads were counted in genomic bins and normalized by the median. The foldchange and coverage were […]


Subependymal giant cell astrocytomas in Tuberous Sclerosis Complex have consistent TSC1/TSC2 biallelic inactivation, and no BRAF mutations

PMCID: 5707039
PMID: 29221145
DOI: 10.18632/oncotarget.20764
call_split See protocol

[…] tion analysis for single nucleotide variants (SNV) was performed using MuTect v1.1.4 and annotated by Variant Effect Predictor (VEP) [, ]. Insertions and deletions were called using Indel Locator and SomaticIndelDetector tool [, ]. MuTect was run in paired mode using a CEPH sample as a normal since normal DNA samples were not available, and a germline variant filter was then applied. Variants were […]


Activating mutation of PDGFRB gene in a rare cardiac undifferentiated intimal sarcoma of the left atrium: a case report

PMCID: 5655321
PMID: 29113426
DOI: 10.18632/oncotarget.20700
call_split See protocol

[…] performed on tumor sample and control normals to identify point mutations/single nucleotide variants (SNVs) and small insertions/deletion (indels). MuTect (version 1.1.4) was used for SNV calling and SomaticIndelDetector, a tool in GATKv.2.3.9, was used for detecting indel events. Variants were subsequently annotated using Annovar, and annotations relative to the canonical transcript for each gene […]


Genomic profiles of a hepatoblastoma from a patient with Beckwith Wiedemann syndrome with uniparental disomy on chromosome 11p15 and germline mutation of APC and PALB2

PMCID: 5696154
PMID: 29190888
DOI: 10.18632/oncotarget.20515

[…] ing the Illumina HiSeq2000 platform and the Burrows-Wheeler aligner was used to align the sequencing reads onto the human reference genome (hg19). Somatic variants were identified using MuTect [] and SomaticIndelDetector [] for point mutations and indels, respectively. Germline variants were identified using GATK HaplotypeCaller. All variants were annotated using ANNOVAR []. Mutation rates and spe […]

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