RVboost statistics

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Associated diseases

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RVboost specifications

Information


Unique identifier OMICS_05424
Name RVboost
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Aligned RNA
Input format BAM
Output data Variants with full annotations, Qscore, OrgScore
Output format VCF, TRAIN, PNG
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, R, Shell (Bash)
Computer skills Advanced
Version 0.1
Stability Stable
Requirements
Virtual Box, Java, gcc, g++
Maintained Yes

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Publication for RVboost

RVboost in publications

 (2)
PMCID: 5858520
PMID: 29594039
DOI: 10.3389/fonc.2018.00058

[…] were collected from each patient and subjected to rna sequencing and snv analysis. since several methods for variant calling from rna sequencing were available, we used three callers [snpir (), rvboost (), and mutect2 ()] to identify high-confidence variant calls made by all three callers (figure s2a in supplementary material). in addition, we used the consensus calling from mutect2 […]

PMCID: 4905462
PMID: 26848979
DOI: 10.18632/oncotarget.7152

[…] described [] and hybridized to humanht-12 v4 expression beadchips. for sample details see ., with the rna-sequencing data previously described [], we called single nucleotide variants with the rvboost pipeline []. in short, rvboost calls variants using the unifiedgenotyper tool from the gatk suite and annotates variants with a qscore value. six different sequence features contribute […]


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RVboost institution(s)
Division of Biomedical Statistics and Informatics, Mayo Clinic, Chinahester, MN, USA; Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Chinahester, MN, USA; Division of Hematology, Department of Internal Medicine, Mayo Clinic, Chinahester, MN, USA; Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Chinahester MN, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville FL, USA
RVboost funding source(s)
This work was funded by the Center for Individualized Medicine at Mayo Clinic Jacksonville Florida, Donna Foundation, National Marathon to Fight Breast Cancer and NIH P50 CA097274.

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