VarSifter statistics

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Associated diseases

Associated diseases

VarSifter specifications

Information


Unique identifier OMICS_05447
Name VarSifter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline James C. Mullikin <>

Publication for VarSifter

VarSifter in pipeline

2017
PMCID: 5354242
PMID: 28301468
DOI: 10.1371/journal.pone.0169687

[…] (url: http://evs.gs.washington.edu/evs/)), dbsnp [] and exac [] using gatk’s variantannotator. snpsift/snpeff [] was used to complete annotation from dbsnp and dbnsfp. the variants were uploaded to varsifter [] and non-coding variants were removed, along with those not passing hard-filtering, and variants with a maf>2% in either the global or south asian population. the resulting list […]


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VarSifter in publications

 (17)
PMCID: 5777758
PMID: 29383146
DOI: 10.18632/oncotarget.22914

[…] sequence variants were annotated to determine genic context (i.e., non-synonymous, missense, splicing) using annovar [], and summarized using spreadsheets and a genomic data visualization tool, varsifter []. additional contextual information from other studies was added, including allele frequency from 1000 genomes [] and the nhlbi exome sequence project [], in silico function impact […]

PMCID: 5656749
PMID: 29085913
DOI: 10.1128/mSphere.00393-17

[…] parameters. the gatk unified genotyper () was used to call all locations of allele frequencies. for 09-cb1 and r3 and s3 bulks, snpeff 3.0 was used to call effects for filtered variants. finally, varsifter 1.5 () was used to inspect final genotype calls for coherence. igv 2.3 () was used to visualize the polymorphisms (snps and indels) per cross project, respectively. for cross 2, […]

PMCID: 5495032
PMID: 28679688
DOI: 10.1101/mcs.a001321

[…] genotypes were called using only those sequence bases with phred base qualities of at least q20 using most probable genotype () (mpg) and an mpg score of ≥10. filters were applied using the varsifter next-gen variant analysis software (). variants were filtered for nonsynonymous, splice-site, frameshift, and nonsense alterations. to filter for rare variants, the clinseq cohort (1001 […]

library_books

HSP and deafness

PMCID: 5432370
PMID: 28534044
DOI: 10.1212/NXG.0000000000000151

[…] was performed at the nih intramural sequencing center using the illumina (san diego, ca) truseq exome enrichment kit, and illumina hiseq 2500 sequencing instruments. variants were analyzed using varsifter and searched for in the national heart, lung, and blood institute exome sequencing project database (evs.gs.washington.edu/evs/) and exome aggregation consortium database […]

PMCID: 5354242
PMID: 28301468
DOI: 10.1371/journal.pone.0169687

[…] (url: http://evs.gs.washington.edu/evs/)), dbsnp [] and exac [] using gatk’s variantannotator. snpsift/snpeff [] was used to complete annotation from dbsnp and dbnsfp. the variants were uploaded to varsifter [] and non-coding variants were removed, along with those not passing hard-filtering, and variants with a maf>2% in either the global or south asian population. the resulting list […]


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VarSifter institution(s)
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

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