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Vancouver Short Read Analysis specifications

Information


Unique identifier OMICS_13970
Name Vancouver Short Read Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format GFF3, SAM, SNVmix, VCF
Output data An image for visualize up to four groupings of data (RNA, exon capture, whole genome and controls)
Output format SVG
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Database management system PostgreSQL
License GNU General Public License version 3.0
Computer skills Advanced
Version 4.0.16
Stability Stable
Maintained Yes

Subtools


  • FindPeaks
  • Variations Database

Download


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Versioning


No version available

Maintainer


  • person_outline Anthony Fejes <>

Additional information


An old version of FindPeaks is also available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks

Publications for Vancouver Short Read Analysis

Vancouver Short Read Analysis citations

 (53)
library_books

Identification of genetic variants for clinical management of familial colorectal tumors

2018
PMCID: 5819082
PMID: 29458332
DOI: 10.1186/s12881-018-0533-9

[…] consortium (exac) (http://exac.broadinstitute.org, accessed august 2015) [], genome aggregation database (gnomad) (http://gnomad.broadinstitute.org, accessed october 2017) [], norwegian germline variations database (http://norgene.no/vcf-miner/, accessed october 2017), clinvar (may 2016) [], uniprot knowledgebase (release march 2016) [] and the pfam protein domain database (v29, december […]

library_books

SAC1 degrades its lipid substrate PtdIns4P in the endoplasmic reticulum to maintain a steep chemical gradient with donor membranes

2018
PMCID: 5829913
PMID: 29461204
DOI: 10.7554/eLife.35588.033

[…] note, the sacm1l gene used in this study and previous publications () contains a missense mutation y433f relative to the human genome reference sequence. however, the short genetic variations database (dbsnp) shows that this allele (rs1468542) represents approximately 60% of alleles present in the human population sampled to date. this allele can therefore be viewed […]

library_books

Impaired K+ binding to glial glutamate transporter EAAT1 in migraine

2017
PMCID: 5654970
PMID: 29066757
DOI: 10.1038/s41598-017-14176-4

[…] of slc1a3 revealed a heterozygous nucleotide change c.1159 a > c (nm_004172). the variant was not detected in 100 control chromosomes nor listed in the databases dbsnp (short nucleotide variations database), exac (exome aggregation consortium) and evs (exome variant server). analysis of the parental dna revealed the variant in the father, while dna from other family members […]

library_books

DCTN1 gene analysis in Chinese patients with sporadic amyotrophic lateral sclerosis

2017
PMCID: 5549744
PMID: 28792508
DOI: 10.1371/journal.pone.0182572

[…] mutationtaster (http://www.mutationtaster.org), sift (http://sift.jcvi.org/) programs were used to predict the effects of each mutation on protein function. the short genetic variations database (dbsnp 142), the nhlbi exome variant server (evs), the 1000 genomes project (tgp), and the exome aggregation consortium (exac) databases were checked for the presence […]

library_books

Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome

2017
PMCID: 5549384
PMID: 28789634
DOI: 10.1186/s12864-017-4000-3

[…] and online databanks and bioinformatics tools were used. variation viewer [] (release 1.5) was used as a tool for navigating variant data in ncbi’s databases: dbsnp (snp and multiple small-scale variations database, release 149), dbvar (genomic structural variation database, release december 2015) and clinvar (data base for genomic variation and its relationship to human health, release […]

library_books

Variation of mutant allele frequency in NRAS Q61 mutated melanomas

2017
PMCID: 5494128
PMID: 28668077
DOI: 10.1186/s12895-017-0061-x

[…] for patients with several samples available, the m%nras used was that obtained from the first metastasis.table 1 , eight microsatellite markers were selected from the ncbi dbsnp short genetic variations database and analyzed by aflp. their positions are showed in fig. , and the primers used in table . no highly heterozygous microsatellite was identified within nras gene; thus the genetic […]


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Vancouver Short Read Analysis institution(s)
Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
Vancouver Short Read Analysis funding source(s)
This project was supported by the Michael Smith Foundation for Health Research and the Genome British Columbia.

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