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SNPiR | Identification of genomic variants from RNA-seq data

Identifies single nucleotides polymorphisms (SNPs) in RNA-seq data. SNPiR consists of (1) a modified RNA-seq read-mapping procedure that allows alignment of reads to the reference in a splice-aware manner, (2) variant calling using the Genome Analysis Toolkit (GATK) and (3) vigorous filtering of false-positive calls. The software allows the detection of variants even for lowly expressed genes. It was applied to data from the GM12878 human lymphoblastoid cell line and peripheral blood mononuclear cells (PBMCs) from another healthy individual.

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SNPiR forum

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SNPiR classification

SNPiR specifications

Unique identifier:
OMICS_01362
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable
Software type:
Application/Script, Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes

SNPiR distribution

versioning

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No versioning.

SNPiR support

Maintainer

  • Jin Billy Li <>

Credits

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Publications

Institution(s)

Department of Genetics, Stanford University, Stanford, CA, USA

Funding source(s)

Supported by a fellowship from the German Academic Exchange Service, the Stanford Genome Training Program, funded by the National Institutes of Health (NIH), a Stanford Graduate Fellowship, the Stanford University Department of Genetics, NIH, and Ellison Medical Foundation.

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