Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

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.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

SNPiR forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

SNPiR classification

SNPiR specifications

Unique identifier:
Command line interface
Operating system:
Software type:
Application/Script, Package/Module
Restrictions to use:
Computer skills:

SNPiR distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

SNPiR support


  • Jin Billy Li <>


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



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.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.