SnpSift statistics

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Protocols

SnpSift specifications

Information


Unique identifier OMICS_23967
Name SnpSift
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 4.3s
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Douglas M. Ruden

Publication for SnpSift

SnpSift citations

 (104)
library_books

Genetic alterations analysis in prognostic stratified groups identified TP53 and ARID1A as poor clinical performance markers in intrahepatic cholangiocarcinoma

2018
Sci Rep
PMCID: 5940669
PMID: 29740198
DOI: 10.1038/s41598-018-25669-1

[…] t frequency for indels was set to 0.05 instead of 0.15; complex variant detection was enabled). Called variants were annotated using a custom pipeline based on vcflib (https://github.com/ekg/vcflib), SnpSift, the Variant Effect Predictor (VEP) software and NCBI RefSeq database. Confident somatic mutations were obtained from annotated variants by: i) filtering-out germline mutations identified in m […]

call_split

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia

2018
PLoS One
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860
call_split See protocol

[…] thub.io/picard). SNPs were identified with Freebayes v1.0.2.29 [] using a list (-L) to compare all genomes from a single subject compared to the reference sequence (USA300_FPR3757) and filtered using SnpSift [] for the following qualities (MQM > 20 and DP > 40). For each subject, the SnpSift call for Reference (isRef) and Variant (isVar) was completed in a stepwise manner to determine how mutation […]

call_split

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia

2018
Oncotarget
PMCID: 5929421
PMID: 29731978
DOI: 10.18632/oncotarget.24808
call_split See protocol

[…] followed by de-duplication, re-calibration and variant calling with the Genome Analysis Toolkit (GATK) Best Practices workflow (v3.5.0) []. The resulting variant calls were annotated using SnpEff and SnpSift (v4.2) followed by filtering and analysis using in-house Python and R scripts [, ]. […]

library_books

Bordetella pseudohinzii targets cilia and impairs tracheal cilia driven transport in naturally acquired infection in mice

2018
Sci Rep
PMCID: 5890243
PMID: 29632402
DOI: 10.1038/s41598-018-23830-4

[…] e quality clipped as described before and mapped onto aforementioned Bordetella genomes with bowtie2. Afterwards, SNPs were detected via Samtools and BCFtools toolkits. Called SNPs were filtered with SnpSift, and finally annotated with SnpEff. Finally, for comparative analyses GECO and EDGAR were used with the following genomes: B. avium 197NT (NC_010645), B. hinzii F582T (NZ_CP012076), B. hinzii […]

call_split

Mob2 Insufficiency Disrupts Neuronal Migration in the Developing Cortex

2018
PMCID: 5857600
PMID: 29593499
DOI: 10.3389/fncel.2018.00057
call_split See protocol

[…] the Exome Aggregation Consortium (ExAC) via the GATK VariantAnnotator. All alignments with loci bearing putative de novo variants were extracted from the multisample VCF using GATK SelectVariants and SnpSift v.4.1L (SnpEff) that met the following criteria: (1) the read depth should be ≥8 within the patient; (2) at least 20% of the reads should carry the alternate allele; (3) <5% of the reads in ei […]

call_split

A missense mutation in MYH1 is associated with susceptibility to immune mediated myositis in Quarter Horses

2018
PMCID: 5838957
PMID: 29510741
DOI: 10.1186/s13395-018-0155-0
call_split See protocol

[…] SnpEFF [] and SnpSift [] were used to predict the functional effects of detected variants across the genome and within chr11 candidate region and filter by segregation using Fisher’s exact test. Variants were filte […]

Citations

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SnpSift institution(s)
Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, C.S. Mott Center, Detroit, MI, USA; School of Computer Science and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada; Department of Computer Sciences, Wayne State University, Detroit, MI, USA
SnpSift funding source(s)
Supported by a Michigan Core Technology grant from the State of Michigan’s 21st Century Fund Program to the Wayne State University Applied Genomics Technology Center; by the Environmental Health Sciences Center in Molecular and Cellular Toxicology with Human Applications Grant P30 ES06639 at Wayne State University, NIH R01 grants (ES012933), and DK071073.

SnpSift review

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Arup Ghosh

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Desktop
Filter VCF files with specific criteria and compare control and treated sample sets using SnpSift after annotating with SnpEff.