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RADIA specifications

Information


Unique identifier OMICS_08675
Name RADIA
Alternative name RNA and DNA Integrated Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A sequence data.
Input format BAM
Output data Some variant calls.
Output format VCF
Operating system Unix/Linux
Programming languages Python
License GNU Affero General Public License version 3
Computer skills Advanced
Version 1.1.3
Stability Stable
Requirements
SAMtools, PySam API, BLAT, SnpEff
Maintained Yes

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Documentation


Maintainer


  • person_outline David Haussler

Publication for RNA and DNA Integrated Analysis

RADIA citations

 (4)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] vs. non-reference and tumor vs. normal). A small p-value indicates that non-reference reads are disproportionately distributed in the pair of samples and therefore suggests somatic variant. qSNP and RADIA apply sets of heuristic rules to label somatic variants that are sufficiently observed in tumor but weakly or not observed in normal. If RNA-seq data from the same patient are available, RADIA w […]

library_books

A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations

2018
Front Immunol
PMCID: 5797543
PMID: 29441070
DOI: 10.3389/fimmu.2018.00099

[…] (). The haplotype for a sample is decided based on a consensus decision of the three input haplotypes. Somatic point mutations were called using a panel of five mutation callers, MuTECT (), MuSE (), RADIA (), SomaticSniper (), and Strelka (). Since most mutation callers are DNA centric, we allow mutations rejected by up to two of the callers through this first filter. The vcf of first-pass mutant […]

library_books

Punctuated evolution of canonical genomic aberrations in uveal melanoma

2018
Nat Commun
PMCID: 5760704
PMID: 29317634
DOI: 10.1038/s41467-017-02428-w

[…] default settings for UNCeqR, mutations were filtered if both DNA and RNA alternate tumor read counts were < 3, < 20% of the total tumor read count, or the gene fell within the blacklist suggested by Radia. For mutations called by Varscan2 or MuTect2, mutations were further filtered out if both alternate tumor read counts were < 3 and the minor allele frequency (MAF) was < 20%. For all sequencing […]

library_books

A Novel Secreted Protein, MYR1, Is Central to Toxoplasma’s Manipulation of Host Cells

2016
MBio
PMCID: 4742717
PMID: 26838724
DOI: 10.1128/mBio.02231-15

[…] e genome of Toxoplasma gondii GT1 strain downloaded from ToxoDB (release 10.0) (). Single nucleotide variants (SNVs) that were present in mutant strains and not in the wild type were identified using RADIA (https://github.com/aradenbaugh/radia/) (). RADIA used the SAMtools () (mpileup command [version 0.1.18]) to examine the base calls at each locus of the genome in parallel for the wild type and […]

Citations

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RADIA institution(s)
University of California Santa Cruz Genomics Institute, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA

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