SNPiR protocols

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SNPiR specifications


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


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  • person_outline Jin Billy Li <>

Publication for SNPiR

SNPiR in pipeline

PMCID: 4506401
PMID: 26084335
DOI: 10.1186/s13059-015-0692-3

[…] -filtername qd -filter “qd < 2.0” \). after removal of variant call quality q < 20, further filtering was applied to snvs that were considered to be potential false positives in rna-seq by snpir []. we regarded only those snvs which overlapped with wes as true positives. the overall process of calling and filtering the variants is summarized in figure s4a in additional file ., rss […]

SNPiR in publications

PMCID: 5858520
PMID: 29594039
DOI: 10.3389/fonc.2018.00058

[…] from the bowel 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 […]

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] to variation in expression levels; and 4) rna editing sites being confused as dna mutations., currently there are at least variant callers that accept rna-seq data: radia, seurat, vardict, varscan2, snpir, and esnv-detect , , , , , . radia and seurat do not analyze rna-seq data alone, but integrate rna-seq with matched tumor-normal dna from the same patient to improve the accuracy. radia showed […]

PMCID: 5339410
PMID: 28185911
DOI: 10.1016/j.gpb.2016.12.002

[…] . global gene fusions were further filtered to include those with ≥10 reads spanning the break-point . snps were called using gatk, samtools, and bedtools according to the pipeline described in snpir . the transcriptome data had been deposited in the genome sequencing archive (accession no. prjca000343)., unsupervised hierarchical clustering of filtered gene expression profiles (fpkm >1) […]

PMCID: 4939914
PMID: 27245094
DOI: 10.1080/15592294.2016.1184805

[…] kidney, liver, skeletal muscle and placenta of the 4 conceptuses (control #1, #2, #3, and #4; table s1) and were aligned to the custom b. t. indicus/b. t. taurus diploid genome. we adapted the snpir pipeline to identify snps using all rnaseq reads from each conceptus. to minimize false positive snp calls, in addition to the default pipeline, bwa, we also mapped the reads using hisat2 […]

PMCID: 4671599
PMID: 26641247
DOI: 10.1371/journal.pone.0144440

[…] has been detected between the amino acids m1 and a19, and an inhibitory region (pro-region) was found to exist between the amino acids a20 and i137., the pro-region contained the strongly conserved snpir, erfnin (ex3rx3fx2nx3ix3n) and anfd (axnxfxd) motifs. the catalytic region of the protein was comprised between the amino acids l138 and a355. the predicted molecular mass and pi […]

SNPiR institution(s)
Department of Genetics, Stanford University, Stanford, CA, USA
SNPiR 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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