VARIANT protocols

VARIANT specifications

Information


Unique identifier OMICS_00193
Name VARIANT
Alternative name VARIant ANalysis Tool
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Additional information


http://docs.bioinfo.cipf.es/projects/variant

VARIANT IN pipelines

 (3)
2017
PMCID: 5655919
PMID: 28748566
DOI: 10.1111/bjh.14863

[…] performed by a maximum likelihood approach on a bayesian model. variants were called with a minimum of 9 ×  coverage, 3 counts and 25% frequency. variants were further filtered using the ingenuity variant analysis tool (qiagen), excluding the low quality scores and variants (>1% in background population), and including variants found within the 87‐gene list and variants associated […]

2014
PMCID: 4299714
PMID: 25629078
DOI: 10.1002/mgg3.111

[…] platform at 75 base paired-end sequencing (san diego, ca). sequence output was inspected and aligned against human reference genome hg19, and variants were filtered and annotated using ingenuity variant analysis tool by the university of michigan bioinformatics core. in the yale center for genome analysis, the exome sequencing and subsequent analysis were modified from a previous report […]

2011
PMCID: 3287936
PMID: 22373203
DOI: 10.1186/1753-6561-5-S9-S94

[…] in plink., we use the collapsing method proposed by li and leal [4] and morris and zeggini [8] to identify possible variants among rare snps. for this analysis we use the ccravat (case-control rare variant analysis tool) software package [13]. the collapsing method is as follows: first, we divide the markers into groups on the basis of predefined criteria (either genes or sliding windows […]

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