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SomaticIndelDetector specifications

Information


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

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SomaticIndelDetector citations

 (36)
library_books

The molecular landscape of synchronous colorectal cancer reveals genetic heterogeneity

2018
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 […]

library_books

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

2018
PMCID: 5903820
PMID: 29422544
DOI: 10.1038/emm.2017.265

[…] 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 […]

library_books

Quantitative radiomic profiling of glioblastoma represents transcriptomic expression

2018
PMCID: 5814216
PMID: 29464076
DOI: 10.18632/oncotarget.23975

[…] using samtools, picard version 1.73, and genome analysis toolkit (gatk version 2.5.2.), the initial alignment bam files were subjected to conventional preprocessing we used mutect (version 1.1.4), somaticindeldetector (gatk version 2.2) and variant effect predictor (vep)., the ngcgh python package was used to generate acgh-like data from whole exome sequencing (wes). matching normal samples […]

library_books

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

2018
PMCID: 5871330
PMID: 29580384
DOI: 10.7554/eLife.31347.034

[…] 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 […]

library_books

Blood collection in cell stabilizing tubes does not impact germline DNA quality for pediatric patients

2017
PMCID: 5716571
PMID: 29206863
DOI: 10.1371/journal.pone.0188835

[…] loci among samples obtained from the same patient., variant analysis for single nucleotide variants (snv) was performed using mutect v1.1.4 and annotated by variant effect predictor (vep). the somaticindeldetector tool from gatk was used for indel calling [, ]. mutect was run in paired mode using sequencing data generated from human cell line ceph1408 as the project normal. samples […]

library_books

A case report of tongue metastasis from lung squamous cell carcinoma and literature review

2017
PMCID: 5738010
PMID: 28984774
DOI: 10.1097/MD.0000000000008208

[…] recalibration. somatic single nucleotide substitutions were called by combined using of varscan2 (version 2.3.7) and mutect (version 1.1.7), and somatic small indels were detected by combined use of somaticindeldetector (gatk version 2.3.9) and varscan2 (version 2.3.7)., fisher exact test was performed on every locus in which a second allele was detected, to improve the sensitivity of mutation […]


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